src Directory Reference

Directory dependency graph for /tmp/jenkins/workspace/ESPResSo/src/:

Directories
directory	mpifake
directory	object-in-fluid
directory	tcl
Files
file	acconfig.h [code]
file	adresso.c [code]
	This is the place for adaptive resolution scheme Implementation of adresso.h.
file	adresso.h [code]
	This is the place for adaptive resolution scheme (adress) Implementation of adresso.h.
file	angle.c [code]
	Implementation of angle.h.
file	angle.h [code]
	Routines to calculate the angle energy or/and and force for a particle triple.
file	angle_cosine.c [code]
	Implementation of angle_cosine.h.
file	angle_cosine.h [code]
	Routines to calculate the angle energy or/and and force for a particle triple.
file	angle_cossquare.c [code]
	Implementation of angle.h.
file	angle_cossquare.h [code]
	Routines to calculate the angle energy or/and and force for a particle triple.
file	angle_harmonic.c [code]
	Implementation of angle.h.
file	angle_harmonic.h [code]
	Routines to calculate the angle energy or/and and force for a particle triple.
file	angledist.c [code]
	Implementation of angledist.h.
file	angledist.h [code]
	Routines to calculate the angle and distance dependent (from a constraint) energy or/and and force for a particle triple.
file	bmhtf-nacl.c [code]
	Implementation of bmhtf-nacl.h.
file	bmhtf-nacl.h [code]
	Routines to calculate the Born-Meyer-Huggins-Tosi-Fumi energy and/or force for a particle pair.
file	buckingham.c [code]
	Implementation of buckingham.h.
file	buckingham.h [code]
	Routines to calculate the Buckingham energy and/or force for a particle pair.
file	cells.c [code]
	This file contains functions for the cell system.
file	cells.h [code]
	This file contains everything related to the cell structure / cell system.
file	collision.c [code]
file	collision.h [code]
file	comfixed.c [code]
	Implementation of comfixed.h.
file	comfixed.h [code]
	Routines to enable comfixed.
file	comforce.c [code]
	Implementation of comforce.h.
file	comforce.h [code]
	Routines for center of mass forces.
file	communication.c [code]
file	communication.h [code]
	This file contains the asynchronous MPI communication.
file	config-doxygen.h [code]
file	config-features.c [code]
file	config-features.h [code]
file	config-version.c [code]
file	config.h [code]
	This file contains the defaults for Espresso.
file	constraint.c [code]
	Implementation of constraint.h, here it's just the parsing stuff.
file	constraint.h [code]
	Routines for handling of constraints.
file	cuda_init.cu [code]
file	cuda_init.h [code]
file	debug.c [code]
	Implements the malloc replacements as described in debug.h.
file	debug.h [code]
	This file controls debug facilities.
file	debye_hueckel.c [code]
	Implementation of debye_hueckel.h.
file	debye_hueckel.h [code]
	Routines to calculate the Debye_Hueckel Energy or/and Debye_Hueckel force for a particle pair.
file	dihedral.c [code]
	Implementation of dihedral.h.
file	dihedral.h [code]
	Routines to calculate the dihedral energy or/and and force for a particle quadruple.
file	domain_decomposition.c [code]
	This file contains everything related to the cell system: domain decomposition.
file	domain_decomposition.h [code]
	This file contains everything related to the cell system: domain decomposition.
file	dpd.c [code]
	Implementation of dpd.h.
file	dpd.h [code]
	Routines to use dpd as thermostat or pair force T.
file	elc.c [code]
	For more information about ELC, see elc.h.
file	elc.h [code]
	ELC algorithm for long range coulomb interactions.
file	endangledist.c [code]
	Implementation of endangledist.h.
file	endangledist.h [code]
	Routines which apply an angle potential between two particles and a wall constraint At distmax the angle potential is slowly switched on to a maximum at distmin phi0 is constant but could easily be implemented to depend on the distance.
file	energy.c [code]
	Implementation of energy.h.
file	energy.h [code]
	Implementation of the energy calculation.
file	errorhandling.c [code]
	Implementation of errorhandling.h.
file	errorhandling.h [code]
	This file contains the errorhandling code for severe errors, like a broken bond or illegal parameter combinations.
file	fene.c [code]
	Implementation of fene.h.
file	fene.h [code]
	Routines to calculate the FENE Energy or/and FENE force for a particle pair.
file	fft-common.c [code]
	Routines, row decomposition, data structures and communication for the 3D-FFT.
file	fft-common.h [code]
file	fft-dipolar.c [code]
file	fft-dipolar.h [code]
	Routines, row decomposition, data structures and communication for the 3D-FFT.
file	fft.c [code]
	Routines, row decomposition, data structures and communication for the 3D-FFT.
file	fft.h [code]
	Routines, row decomposition, data structures and communication for the 3D-FFT.
file	forcecap.c [code]
	force cap calculation.
file	forcecap.h [code]
file	forces.c [code]
	Force calculation.
file	forces.h [code]
	Force calculation.
file	galilei.c [code]
file	galilei.h [code]
file	gaussian.c [code]
	Implementation of gaussian.h.
file	gaussian.h [code]
	Routines to calculate the Gaussian energy and/or force for a particle pair.
file	gb.c [code]
	Implementation of gb.h.
file	gb.h [code]
	Routines to calculate the Gay-Berne energy and force for a pair of particles.
file	ghmc.c [code]
	For more information see ghmc.h.
file	ghmc.h [code]
	This file contains the implementation of the GHMC (Generalized Hybrid Monte Carlo) thermostat.
file	ghosts.c [code]
	Ghost particles and particle exchange.
file	ghosts.h [code]
	Ghost particles and particle exchange.
file	global.c [code]
	Implementation of global.h.
file	global.h [code]
	This file contains the code for access to globally defined variables using the script command setmd.
file	grid.c [code]
	Domain decomposition for parallel computing.
file	grid.h [code]
	Domain decomposition for parallel computing.
file	halo.c [code]
	Halo scheme for parallelization of lattice algorithms.
file	halo.h [code]
	Halo scheme for parallelization of lattice algorithms.
file	harmonic.c [code]
	Implementation of harmonic.h.
file	harmonic.h [code]
	Routines to calculate the HARMONIC Energy or/and HARMONIC force for a particle pair.
file	hat.c [code]
file	hat.h [code]
file	hertzian.c [code]
	Implementation of hertzian.h.
file	hertzian.h [code]
	Routines to calculate the Hertzian energy and/or force for a particle pair.
file	iccp3m.c [code]
	Detailed Information about the method is included in the corresponding header file iccp3m.h.
file	iccp3m.h [code]
	ICCP3M is a method that allows to take into account the influence of arbitrarliy shaped dielectric interfaces.
file	imd.c [code]
	Implementation of imd.h.
file	imd.h [code]
	The interface with VMD.
file	initialize.c [code]
	Implementation of initialize.h.
file	initialize.h [code]
	This file contains the hook procedures.
file	integrate.c [code]
	Molecular dynamics integrator.
file	integrate.h [code]
	Molecular dynamics integrator.
file	interaction_data.c [code]
	Implementation of interaction_data.h.
file	interaction_data.h [code]
	Various procedures concerning interactions between particles.
file	lattice.c [code]
	Lattice data structures.
file	lattice.h [code]
	Lattice data structures.
file	layered.c [code]
	Implementation of layered.h.
file	layered.h [code]
	The layered cellsystem.
file	lb-boundaries.c [code]
	Boundary conditions for Lattice Boltzmann fluid dynamics.
file	lb-boundaries.h [code]
	Boundary conditions for Lattice Boltzmann fluid dynamics.
file	lb-d3q18.h [code]
	Header file for the lattice Boltzmann D3Q18 model.
file	lb-d3q19.h [code]
	Header file for the lattice Boltzmann D3Q19 model.
file	lb.c [code]
	Lattice Boltzmann algorithm for hydrodynamic degrees of freedom.
file	lb.h [code]
	Header file for lb.c.
file	lbgpu.cu [code]
	Cuda (.cu) file for the Lattice Boltzmann implementation on GPUs.
file	lbgpu.h [code]
	Header file for lbgpu.c.
file	lbgpu_cfile.c [code]
	C file for the Lattice Boltzmann implementation on GPUs.
file	lj.c [code]
file	lj.h [code]
	Routines to calculate the lennard jones energy and/or force for a particle pair.
file	ljangle.c [code]
file	ljangle.h [code]
	Routines to calculate the lennard-jones 12-10 with angular dependance.
file	ljcos.c [code]
file	ljcos.h [code]
	Routines to calculate the lennard jones+cosine energy and/or force for a particle pair.
file	ljcos2.c [code]
file	ljcos2.h [code]
	Routines to calculate the lennard-jones with cosine tail energy and/or force for a particle pair.
file	ljgen.c [code]
	Routines to calculate the generalized lennard jones energy and/or force for a particle pair.
file	ljgen.h [code]
	Routines to calculate the generalized lennard jones energy and/or force for a particle pair.
file	maggs.c [code]
	Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions.
file	maggs.h [code]
	Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions.
file	magnetic_non_p3m_methods.c [code]
	All 3d non P3M methods to deal with the magnetic dipoles.
file	magnetic_non_p3m_methods.h [code]
	Header of all 3d non P3M methods to deal with the magnetic dipoles.
file	mdlc_correction.c [code]
file	mdlc_correction.h [code]
file	metadynamics.c [code]
file	metadynamics.h [code]
	This file contains routines to perform metadynamics.
file	mmm-common.c [code]
	Common parts of the MMM family of methods for the electrostatic interaction, MMM1D, MMM2D and ELC.
file	mmm-common.h [code]
	modified polygamma functions.
file	mmm1d.c [code]
	MMM1D algorithm for long range coulomb interaction.
file	mmm1d.h [code]
	MMM1D algorithm for long range coulomb interactions.
file	mmm2d.c [code]
	MMM2D algorithm for long range coulomb interaction.
file	mmm2d.h [code]
	MMM2D algorithm for long range coulomb interaction in 2d+h geometries.
file	modes.c [code]
	Implementation of modes.h.
file	modes.h [code]
	PLEASE INSERT DESCRIPTION.
file	mol_cut.c [code]
	Implementation of mol_cut.h.
file	mol_cut.h [code]
file	molforces.c [code]
	Routines for calculating and applying trap forces upon molecules.
file	molforces.h [code]
	Routines for calculating and applying trap forces upon molecules.
file	morse.c [code]
	Implementation of morse.h.
file	morse.h [code]
	Routines to calculate the lennard jones energy and/or force for a particle pair.
file	myconfig-default.h [code]
file	myconfig-final.h [code]
file	nemd.c [code]
	For more information see nemd.h.
file	nemd.h [code]
	This file contains the implementation of the NEMD (Non Equilibrium Molecular Dynamics) algorithm.
file	npt.h [code]
	exports for the NPT code, which otherwise is really spread all over...
file	nsquare.c [code]
	Implementation of nsquare.h.
file	nsquare.h [code]
	This file contains the code for a simple n^2 particle loop.
file	overlap.c [code]
	Implementation of overlap.h.
file	overlap.h [code]
	Routines to calculate the energy and/or force for bonds, angles and dihedrals as a sum of N functions in the forms: bonds --- parameter: [N, a_i, b_i, c_i], function: U(bond) = sum_(i=1,N) {a_i*exp[-(bond-b_i)^2 /(c_i^2)]}.
file	p3m-common.c [code]
	P3M main file.
file	p3m-common.h [code]
	common functions for dipolar and charge p3m.
file	p3m-dipolar.c [code]
	P3M algorithm for long range magnetic dipole-dipole interaction.
file	p3m-dipolar.h [code]
	P3M algorithm for long range magnetic dipole-dipole interaction.
file	p3m.c [code]
file	p3m.h [code]
	code for calculating the MDLC (magnetic dipolar layer correction).
file	particle_data.c [code]
	This file contains everything related to particle storage.
file	particle_data.h [code]
	For more information on particle_data, see particle_data.c.
file	polymer.c [code]
	This file contains everything needed to create a start-up configuration of (partially charged) polymer chains with counterions and salt molecules, assigning velocities to the particles and crosslinking the polymers if necessary.
file	polymer.h [code]
	This file contains everything needed to create a start-up configuration of (partially charged) polymer chains with counterions and salt molecules, assigning velocities to the particles and crosslinking the polymers if necessary.
file	polynom.h [code]
	Datatypes and functions for polynomials.
file	pressure.c [code]
	Implementation of pressure.h.
file	pressure.h [code]
	Pressure calculation.
file	random.c [code]
	A random generator.
file	random.h [code]
	A random generator.
file	rattle.c [code]
file	rattle.h [code]
	RATTLE Algorithm (Rattle: A "Velocity" Version of the Shake Algorithm for Molecular Dynamics Calculations, H.C Andersen, J Comp Phys, 52, 24-34, 1983)
file	reaction.c [code]
file	reaction.h [code]
file	reaction_field.c [code]
	Implementation of reaction_field.h.
file	reaction_field.h [code]
	Routines to calculate the Reaction Field Energy or/and force for a particle pair.
file	rotation.c [code]
	Molecular dynamics integrator for rotational motion.
file	rotation.h [code]
	This file contains all subroutines required to process rotational motion.
file	soft_sphere.c [code]
	Implementation of soft_sphere.h.
file	soft_sphere.h [code]
	Routines to calculate the soft-sphere energy and/or force for a particle pair.
file	specfunc.c [code]
	Special functions, see specfunc.h.
file	specfunc.h [code]
	This file contains implementations for some special functions which are needed by the MMM family of algorithms.
file	statistics.c [code]
	This is the place for analysis (so far...).
file	statistics.h [code]
	This file contains the code for statistics on the data.
file	statistics_average.c [code]
file	statistics_average.h [code]
file	statistics_chain.c [code]
	Implementation of statistics_chain.h.
file	statistics_chain.h [code]
	This file contains the code for statistics on the data using the molecule information set with analyse set chains.
file	statistics_cluster.c [code]
	This file contains the necklace cluster algorithm.
file	statistics_cluster.h [code]
	1: This file contains the necklace cluster algorithm.
file	statistics_correlation.c [code]
file	statistics_correlation.h [code]
file	statistics_fluid.c [code]
	Fluid related analysis functions.
file	statistics_fluid.h [code]
	Fluid related analysis functions.
file	statistics_molecule.c [code]
	see statistics_molecule.h
file	statistics_molecule.h [code]
	This file contains the code for statistics on the data using the molecule information set with analyse set, as it is described in the file topology.h.
file	statistics_observable.c [code]
file	statistics_observable.h [code]
file	statistics_wallstuff.c [code]
file	statistics_wallstuff.h [code]
file	steppot.c [code]
	Implementation of steppot.h.
file	steppot.h [code]
	Routines to calculate the smooth step potential energy and/or force for a particle pair.
file	subt_lj.c [code]
	Implementation of subt_lj.h.
file	subt_lj.h [code]
	Routines to subtract the LENNARD-JONES Energy and/or the LENNARD-JONES force for a particle pair.
file	tab.c [code]
	Implementation of tab.h.
file	tab.h [code]
	Routines to calculate the energy and/or force for a particle pair or bonds via interpolating from lookup tables.
file	thermostat.c [code]
	Implementation of thermostat.h.
file	thermostat.h [code]
file	topology.c [code]
	This file contains functions for handling the system topology.
file	topology.h [code]
	This file contains functions for handling the system topology.
file	tunable_slip.c [code]
file	tunable_slip.h [code]
	Routines to generate tunable-slip boundary conditions.
file	tuning.c [code]
	Implementation of tuning.h .
file	tuning.h [code]
	This contains a timing loop for the force calculation.
file	utils.h [code]
	Small functions that are useful not only for one modul.
file	uwerr.c [code]
file	uwerr.h [code]
	PLEASE INSERT DOCUMENTATION.
file	verlet.c [code]
	Verlet list.
file	verlet.h [code]
	This file contains routines to setup and handle interaction pair lists (verlet pair lists) for the non bonded interactions.
file	virtual_sites.c [code]
file	virtual_sites.h [code]
	This file contains routine to handle virtual sites Virtual sites are like particles, but they will be not integrated.
file	virtual_sites_com.c [code]
file	virtual_sites_com.h [code]
file	virtual_sites_relative.c [code]
file	virtual_sites_relative.h [code]
file	vmdsock.c [code]
	This is from NAMD, DO NOT CHANGE!
file	vmdsock.h [code]
	DO NOT CHANGE !!!