File List

Here is a list of all files with brief descriptions:

acconfig.h [code]
adresso.c [code]	This is the place for adaptive resolution scheme Implementation of adresso.h
adresso.h [code]	This is the place for adaptive resolution scheme (adress) Implementation of adresso.h
adresso_tcl.c [code]
adresso_tcl.h [code]
angle.c [code]	Implementation of angle.h
angle.h [code]	Routines to calculate the angle energy or/and and force for a particle triple
angle_cosine.c [code]	Implementation of angle_cosine.h
angle_cosine.h [code]	Routines to calculate the angle energy or/and and force for a particle triple
angle_cosine_tcl.c [code]	Implementation of angle_cosine_tcl.h
angle_cosine_tcl.h [code]	Tcl interface for angle_cosine.h
angle_cossquare.c [code]	Implementation of angle.h
angle_cossquare.h [code]	Routines to calculate the angle energy or/and and force for a particle triple
angle_cossquare_tcl.c [code]	Implementation of angle_cossquare_tcl.h
angle_cossquare_tcl.h [code]	Tcl interface for angle_cossquare.h
angle_harmonic.c [code]	Implementation of angle.h
angle_harmonic.h [code]	Routines to calculate the angle energy or/and and force for a particle triple
angle_harmonic_tcl.c [code]	Implementation of angle_harmonic_tcl.h
angle_harmonic_tcl.h [code]	Tcl interface for angle_harmonic.h
angle_tcl.c [code]	Implementation of angle_tcl.h
angle_tcl.h [code]	Tcl interface for angle.h
angledist.c [code]	Implementation of angledist.h
angledist.h [code]	Routines to calculate the angle and distance dependent (from a constraint) energy or/and and force for a particle triple
angledist_tcl.c [code]	Implementation of angledist_tcl.h
angledist_tcl.h [code]	Tcl interface for angledist.h
area_force_global.c [code]
area_force_global.h [code]	Routines to calculate the AREA_FORCE_GLOBAL energy or/and and force for a particle triple (triangle from mesh)
area_force_global_tcl.c [code]
area_force_global_tcl.h [code]
area_force_local.c [code]
area_force_local.h [code]	Routines to calculate the AREA_FORCE_LOCAL energy or/and and force for a particle triple (triangle from mesh)
area_force_local_tcl.c [code]
area_force_local_tcl.h [code]
bending_force.c [code]
bending_force.h [code]	Routines to calculate the bending_force energy or/and and force for a particle quadruple (two triangles that have 2 particles in common)
bending_force_tcl.c [code]
bending_force_tcl.h [code]
bin_tcl.c [code]
binary_file_tcl.c [code]	Implementation of binary_file_tcl.h
binary_file_tcl.h [code]	This file defines a binary file format for the particle data
blockfile_tcl.c [code]	Implements the blockfile command for writing Tcl-formatted data files
bmhtf-nacl.c [code]	Implementation of bmhtf-nacl.h
bmhtf-nacl.h [code]	Routines to calculate the Born-Meyer-Huggins-Tosi-Fumi energy and/or force for a particle pair
bmhtf-nacl_tcl.c [code]	Implementation of bmhtf-nacl_tcl.h
bmhtf-nacl_tcl.h [code]	Tcl interface for bmhtf-nacl.h
buckingham.c [code]	Implementation of buckingham.h
buckingham.h [code]	Routines to calculate the Buckingham energy and/or force for a particle pair
buckingham_tcl.c [code]	Implementation of buckingham_tcl.h
buckingham_tcl.h [code]	Tcl interface for buckingham.h
cells.c [code]	This file contains functions for the cell system
cells.h [code]	This file contains everything related to the cell structure / cell system
cells_tcl.c [code]
channels_tcl.c [code]
collision.c [code]
collision.h [code]
collision_tcl.c [code]
comfixed.c [code]	Implementation of comfixed.h
comfixed.h [code]	Routines to enable comfixed
comfixed_tcl.c [code]	Implementation of comfixed_tcl.h
comfixed_tcl.h [code]	Tcl interface for comfixed.h
comforce.c [code]	Implementation of comforce.h
comforce.h [code]	Routines for center of mass forces
comforce_tcl.c [code]	Implementation of comforce_tcl.h
comforce_tcl.h [code]	Tcl interface for comforce.h
communication.c [code]
communication.h [code]	This file contains the asynchronous MPI communication
config-doxygen.h [code]
config-features.c [code]
config-features.h [code]
config-version.c [code]
config.h [code]	This file contains the defaults for Espresso
config_tcl.c [code]	Code_info and version stuff
constraint.c [code]	Implementation of constraint.h, here it's just the parsing stuff
constraint.h [code]	Routines for handling of constraints
constraint_tcl.c [code]
constraint_tcl.h [code]
cuda_common.cu [code]
cuda_common.h [code]
cuda_common_cfile.c [code]
cuda_init.cu [code]
cuda_init.h [code]
cuda_init_tcl.c [code]
debug.c [code]	Implements the malloc replacements as described in debug.h
debug.h [code]	This file controls debug facilities
debye_hueckel.c [code]	Implementation of debye_hueckel.h
debye_hueckel.h [code]	Routines to calculate the Debye_Hueckel Energy or/and Debye_Hueckel force for a particle pair
debye_hueckel_tcl.c [code]	Implementation of debye_hueckel_tcl.h
debye_hueckel_tcl.h [code]	Tcl interface for debye_hueckel.h
dihedral.c [code]	Implementation of dihedral.h
dihedral.h [code]	Routines to calculate the dihedral energy or/and and force for a particle quadruple
dihedral_tcl.c [code]	Parser for the dihedral potential
dihedral_tcl.h [code]	Tcl interface for dihedral.h
domain_decomposition.c [code]	This file contains everything related to the cell system: domain decomposition
domain_decomposition.h [code]	This file contains everything related to the cell system: domain decomposition
domain_decomposition_tcl.c [code]
domain_decomposition_tcl.h [code]
dpd.c [code]	Implementation of dpd.h
dpd.h [code]	Routines to use dpd as thermostat or pair force T
dpd_tcl.c [code]
dpd_tcl.h [code]
elc.c [code]	For more information about ELC, see elc.h
elc.h [code]	ELC algorithm for long range coulomb interactions
elc_tcl.c [code]	Implementation of elc_tcl.h
elc_tcl.h [code]	Tcl interface for elc.h
endangledist.c [code]	Implementation of endangledist.h
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
endangledist_tcl.c [code]	Implementation of endangledist_tcl.h
endangledist_tcl.h [code]	Tcl interface for endangledist.h
energy.c [code]	Implementation of energy.h
energy.h [code]	Implementation of the energy calculation
energy_tcl.c [code]	Implements the analyze energy command
errorhandling.c [code]	Implementation of errorhandling.h
errorhandling.h [code]	This file contains the errorhandling code for severe errors, like a broken bond or illegal parameter combinations
fene.c [code]	Implementation of fene.h
fene.h [code]	Routines to calculate the FENE Energy or/and FENE force for a particle pair
fene_tcl.c [code]	Implementation of fene_tcl.h
fene_tcl.h [code]	Tcl interface for fene.h
fft-common.c [code]	Routines, row decomposition, data structures and communication for the 3D-FFT
fft-common.h [code]
fft-dipolar.c [code]
fft-dipolar.h [code]	Routines, row decomposition, data structures and communication for the 3D-FFT
fft.c [code]	Routines, row decomposition, data structures and communication for the 3D-FFT
fft.h [code]	Routines, row decomposition, data structures and communication for the 3D-FFT
forcecap.c [code]	Force cap calculation
forcecap.h [code]
forcecap_tcl.c [code]
forcecap_tcl.h [code]
forces.c [code]	Force calculation
forces.h [code]	Force calculation
galilei.c [code]
galilei.h [code]
galilei_tcl.c [code]
galilei_tcl.h [code]
gaussian.c [code]	Implementation of gaussian.h
gaussian.h [code]	Routines to calculate the Gaussian energy and/or force for a particle pair
gaussian_tcl.c [code]	Implementation of gaussian_tcl.h
gaussian_tcl.h [code]	Tcl interface for gaussian.h
gb.c [code]	Implementation of gb.h
gb.h [code]	Routines to calculate the Gay-Berne energy and force for a pair of particles
gb_tcl.c [code]	Implementation of gb_tcl.h
gb_tcl.h [code]	Tcl interface for gb.h
ghmc.c [code]	For more information see ghmc.h
ghmc.h [code]	This file contains the implementation of the GHMC (Generalized Hybrid Monte Carlo) thermostat
ghmc_tcl.c [code]	For more information see ghmc_tcl.h
ghmc_tcl.h [code]	This file contains the tcl interface for the GHMC (Generalized Hybrid MOnte Carlo) thermostat
ghosts.c [code]	Ghost particles and particle exchange
ghosts.h [code]	Ghost particles and particle exchange
global.c [code]	Implementation of global.h
global.h [code]	This file contains the code for access to globally defined variables using the script command setmd
global_tcl.c [code]	Implementation of global_tcl.h
global_tcl.h [code]
grid.c [code]	Domain decomposition for parallel computing
grid.h [code]	Domain decomposition for parallel computing
grid_tcl.c [code]
grid_tcl.h [code]
halo.c [code]	Halo scheme for parallelization of lattice algorithms
halo.h [code]	Halo scheme for parallelization of lattice algorithms
harmonic.c [code]	Implementation of harmonic.h
harmonic.h [code]	Routines to calculate the HARMONIC Energy or/and HARMONIC force for a particle pair
harmonic_tcl.c [code]	Implementation of harmonic_tcl.h
harmonic_tcl.h [code]	Tcl interface for harmonic.h
hat.c [code]
hat.h [code]
hat_tcl.c [code]	Implementation of hat_tcl.h
hat_tcl.h [code]	Tcl interface for hat.h
hertzian.c [code]	Implementation of hertzian.h
hertzian.h [code]	Routines to calculate the Hertzian energy and/or force for a particle pair
hertzian_tcl.c [code]	Implementation of hertzian_tcl.h
hertzian_tcl.h [code]	Tcl interface for hertzian.h
iccp3m.c [code]	Detailed Information about the method is included in the corresponding header file iccp3m.h
iccp3m.h [code]	ICCP3M is a method that allows to take into account the influence of arbitrarliy shaped dielectric interfaces
iccp3m_tcl.c [code]
iccp3m_tcl.h [code]
imd.c [code]	Implementation of imd.h
imd.h [code]	The interface with VMD
imd_tcl.c [code]
initialize.c [code]	Implementation of initialize.h
initialize.h [code]	This file contains the hook procedures
initialize_interpreter.c [code]
integrate.c [code]	Molecular dynamics integrator
integrate.h [code]	Molecular dynamics integrator
integrate_tcl.c [code]
integrate_tcl.h [code]
interaction_data.c [code]	Implementation of interaction_data.h
interaction_data.h [code]	Various procedures concerning interactions between particles
interaction_data_tcl.c [code]
interaction_data_tcl.h [code]
lattice.c [code]	Lattice data structures
lattice.h [code]	Lattice data structures
layered.c [code]	Implementation of layered.h
layered.h [code]	The layered cellsystem
lb-boundaries.c [code]	Boundary conditions for Lattice Boltzmann fluid dynamics
lb-boundaries.h [code]	Boundary conditions for Lattice Boltzmann fluid dynamics
lb-boundaries_tcl.c [code]	Boundary conditions parser file for Lattice Boltzmann fluid dynamics
lb-d3q18.h [code]	Header file for the lattice Boltzmann D3Q18 model
lb-d3q19.h [code]	Header file for the lattice Boltzmann D3Q19 model
lb.c [code]	Lattice Boltzmann algorithm for hydrodynamic degrees of freedom
lb.h [code]	Header file for lb.c
lb_tcl.c [code]	TCL Interface for the Lattice Boltzmann algorithm for hydrodynamic degrees of freedom
lb_tcl.h [code]
lbgpu.cu [code]	Cuda (.cu) file for the Lattice Boltzmann implementation on GPUs
lbgpu.h [code]	Header file for lbgpu.c
lbgpu_cfile.c [code]	C file for the Lattice Boltzmann implementation on GPUs
lj.c [code]
lj.h [code]	Routines to calculate the lennard jones energy and/or force for a particle pair
lj_tcl.c [code]
lj_tcl.h [code]
ljangle.c [code]
ljangle.h [code]	Routines to calculate the lennard-jones 12-10 with angular dependance
ljangle_tcl.c [code]
ljangle_tcl.h [code]
ljcos.c [code]
ljcos.h [code]	Routines to calculate the lennard jones+cosine energy and/or force for a particle pair
ljcos2.c [code]
ljcos2.h [code]	Routines to calculate the lennard-jones with cosine tail energy and/or force for a particle pair
ljcos2_tcl.c [code]
ljcos2_tcl.h [code]
ljcos_tcl.c [code]
ljcos_tcl.h [code]
ljgen.c [code]	Routines to calculate the generalized lennard jones energy and/or force for a particle pair
ljgen.h [code]	Routines to calculate the generalized lennard jones energy and/or force for a particle pair
ljgen_tcl.c [code]
ljgen_tcl.h [code]
maggs.c [code]	Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions
maggs.h [code]	Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions
maggs_tcl.c [code]
maggs_tcl.h [code]
magnetic_non_p3m_methods.c [code]	All 3d non P3M methods to deal with the magnetic dipoles
magnetic_non_p3m_methods.h [code]	Header of all 3d non P3M methods to deal with the magnetic dipoles
magnetic_non_p3m_methods_tcl.c [code]
magnetic_non_p3m_methods_tcl.h [code]
main.c [code]	Main file of Espresso
mdlc_correction.c [code]
mdlc_correction.h [code]
mdlc_correction_tcl.c [code]	Implementation of mdlc_correction_tcl.h
mdlc_correction_tcl.h [code]	Tcl interface for mdlc_correction.h
metadynamics.c [code]
metadynamics.h [code]	This file contains routines to perform metadynamics
metadynamics_tcl.c [code]
metadynamics_tcl.h [code]
mmm-common.c [code]	Common parts of the MMM family of methods for the electrostatic interaction, MMM1D, MMM2D and ELC
mmm-common.h [code]	Modified polygamma functions
mmm1d.c [code]	MMM1D algorithm for long range coulomb interaction
mmm1d.h [code]	MMM1D algorithm for long range coulomb interactions
mmm1d_tcl.c [code]
mmm1d_tcl.h [code]
mmm2d.c [code]	MMM2D algorithm for long range coulomb interaction
mmm2d.h [code]	MMM2D algorithm for long range coulomb interaction in 2d+h geometries
mmm2d_tcl.c [code]
mmm2d_tcl.h [code]
modes.c [code]	Implementation of modes.h
modes.h [code]	PLEASE INSERT DESCRIPTION
mol_cut.c [code]	Implementation of mol_cut.h
mol_cut.h [code]
mol_cut_tcl.c [code]	Implementation of mol_cut_tcl.h
mol_cut_tcl.h [code]	Tcl interface for mol_cut.h
molforces.c [code]	Routines for calculating and applying trap forces upon molecules
molforces.h [code]	Routines for calculating and applying trap forces upon molecules
morse.c [code]	Implementation of morse.h
morse.h [code]	Routines to calculate the lennard jones energy and/or force for a particle pair
morse_tcl.c [code]	TCL interface for the Morse potential
morse_tcl.h [code]
mpi.c [code]	For more information about MPIFake, see mpi.h
mpi.h [code]	This is the MPIfake implementation
myconfig-default.h [code]
myconfig-final.h [code]
nemd.c [code]	For more information see nemd.h
nemd.h [code]	This file contains the implementation of the NEMD (Non Equilibrium Molecular Dynamics) algorithm
nemd_tcl.c [code]
npt.h [code]	Exports for the NPT code, which otherwise is really spread all over..
nsquare.c [code]	Implementation of nsquare.h
nsquare.h [code]	This file contains the code for a simple n^2 particle loop
overlap.c [code]	Implementation of overlap.h
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)]}
overlap_tcl.c [code]	Implementation of overlap_tcl.h
overlap_tcl.h [code]	Tcl interface for overlap.h
p3m-common.c [code]	P3M main file
p3m-common.h [code]	Common functions for dipolar and charge p3m
p3m-dipolar.c [code]	P3M algorithm for long range magnetic dipole-dipole interaction
p3m-dipolar.h [code]	P3M algorithm for long range magnetic dipole-dipole interaction
p3m-dipolar_tcl.c [code]
p3m-dipolar_tcl.h [code]
p3m.c [code]
p3m.h [code]	Code for calculating the MDLC (magnetic dipolar layer correction)
p3m_gpu.cu [code]
p3m_gpu.h [code]
p3m_tcl.c [code]
p3m_tcl.h [code]
parser.c [code]	Implementation of parser.h
parser.h [code]	This file contains macros for parsing the parameters to the 'inter' command
particle_data.c [code]	This file contains everything related to particle storage
particle_data.h [code]	For more information on particle_data, see particle_data.c
particle_data_tcl.c [code]
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
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
polymer_tcl.c [code]
polymer_tcl.h [code]
polynom.h [code]	Datatypes and functions for polynomials
pressure.c [code]	Implementation of pressure.h
pressure.h [code]	Pressure calculation
pressure_tcl.c [code]
pressure_tcl.h [code]
random.c [code]	A random generator
random.h [code]	A random generator
random_tcl.c [code]
random_tcl.h [code]
rattle.c [code]
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)
rattle_tcl.c [code]	Implementation of rattle_tcl.h
rattle_tcl.h [code]	Tcl interface for rattle.h
reaction.c [code]
reaction.h [code]
reaction_field.c [code]	Implementation of reaction_field.h
reaction_field.h [code]	Routines to calculate the Reaction Field Energy or/and force for a particle pair
reaction_field_tcl.c [code]	Implementation of reaction_field_tcl.h
reaction_field_tcl.h [code]	Tcl interface for reaction_field.h
reaction_tcl.c [code]
reaction_tcl.h [code]
rotation.c [code]	Molecular dynamics integrator for rotational motion
rotation.h [code]	This file contains all subroutines required to process rotational motion
scriptsdir.c [code]
soft_sphere.c [code]	Implementation of soft_sphere.h
soft_sphere.h [code]	Routines to calculate the soft-sphere energy and/or force for a particle pair
soft_sphere_tcl.c [code]	Implementation of soft_sphere_tcl.h
soft_sphere_tcl.h [code]	Tcl interface for soft_sphere.h
specfunc.c [code]	Special functions, see specfunc.h
specfunc.h [code]	This file contains implementations for some special functions which are needed by the MMM family of algorithms
statistics.c [code]	This is the place for analysis (so far...)
statistics.h [code]	This file contains the code for statistics on the data
statistics_average.c [code]
statistics_average.h [code]
statistics_chain.c [code]	Implementation of statistics_chain.h
statistics_chain.h [code]	This file contains the code for statistics on the data using the molecule information set with analyse set chains
statistics_chain_tcl.c [code]
statistics_chain_tcl.h [code]
statistics_cluster.c [code]	This file contains the necklace cluster algorithm
statistics_cluster.h [code]	1: This file contains the necklace cluster algorithm
statistics_cluster_tcl.c [code]
statistics_cluster_tcl.h [code]
statistics_correlation.c [code]
statistics_correlation.h [code]
statistics_correlation_tcl.c [code]
statistics_correlation_tcl.h [code]
statistics_fluid.c [code]	Fluid related analysis functions
statistics_fluid.h [code]	Fluid related analysis functions
statistics_fluid_tcl.c [code]
statistics_fluid_tcl.h [code]
statistics_molecule.c [code]	See statistics_molecule.h
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
statistics_observable.c [code]
statistics_observable.h [code]
statistics_observable_tcl.c [code]
statistics_observable_tcl.h [code]
statistics_tcl.c [code]
statistics_tcl.h [code]
statistics_wallstuff.c [code]
statistics_wallstuff.h [code]
statistics_wallstuff_tcl.c [code]	This is the place for analysis (so far...)
statistics_wallstuff_tcl.h [code]
steppot.c [code]	Implementation of steppot.h
steppot.h [code]	Routines to calculate the smooth step potential energy and/or force for a particle pair
steppot_tcl.c [code]	Implementation of steppot_tcl.h
steppot_tcl.h [code]	Tcl interface for steppot.h
stretching_force.c [code]	Implementation of stretching_force.h
stretching_force.h [code]	Routines to calculate the STRETCHING_FORCE Energy or/and STRETCHING_FORCE force for a particle pair
stretching_force_tcl.c [code]
stretching_force_tcl.h [code]
subt_lj.c [code]	Implementation of subt_lj.h
subt_lj.h [code]	Routines to subtract the LENNARD-JONES Energy and/or the LENNARD-JONES force for a particle pair
subt_lj_tcl.c [code]	Implementation of subt_lj_tcl.h
subt_lj_tcl.h [code]	Tcl interface for subt_lj.h
tab.c [code]	Implementation of tab.h
tab.h [code]	Routines to calculate the energy and/or force for a particle pair or bonds via interpolating from lookup tables
tab_tcl.c [code]
tab_tcl.h [code]
thermostat.c [code]	Implementation of thermostat.h
thermostat.h [code]
thermostat_tcl.c [code]
thermostat_tcl.h [code]
topology.c [code]	This file contains functions for handling the system topology
topology.h [code]	This file contains functions for handling the system topology
topology_tcl.c [code]
tunable_slip.c [code]
tunable_slip.h [code]	Routines to generate tunable-slip boundary conditions
tunable_slip_tcl.c [code]	Implementation of tunable_slip_tcl.h
tunable_slip_tcl.h [code]	Tcl interface for tunable_slip.h
tuning.c [code]	Implementation of tuning.h
tuning.h [code]	This contains a timing loop for the force calculation
tuning_tcl.c [code]	Implements the callback for the timings global variable used during tuning of e.g
utils.h [code]	Small functions that are useful not only for one modul
uwerr.c [code]
uwerr.h [code]	PLEASE INSERT DOCUMENTATION
uwerr_tcl.c [code]	Implements the uwerr command
verlet.c [code]	Verlet list
verlet.h [code]	This file contains routines to setup and handle interaction pair lists (verlet pair lists) for the non bonded interactions
virtual_sites.c [code]
virtual_sites.h [code]	This file contains routine to handle virtual sites Virtual sites are like particles, but they will be not integrated
virtual_sites_com.c [code]
virtual_sites_com.h [code]
virtual_sites_com_tcl.c [code]
virtual_sites_com_tcl.h [code]
virtual_sites_relative.c [code]
virtual_sites_relative.h [code]
vmdsock.c [code]	This is from NAMD, DO NOT CHANGE!
vmdsock.h [code]	DO NOT CHANGE !!!
volume_force.c [code]
volume_force.h [code]	Routines to calculate the VOLUME_FORCE energy or/and and force for a particle triple (triangle from mesh)
volume_force_tcl.c [code]
volume_force_tcl.h [code]