Overview of package motion

Methods for changing atomic coordinates

averages_types
Handles the type to compute averages during an MD
bfgs_optimizer
Routines for Geometry optimization using BFGS algorithm
cell_opt
performs CELL optimization
cell_opt_types
Contains type used for a Simulation Cell Optimization
cell_opt_utils
contains a functional that calculates the energy and its derivatives for the geometry optimizer
cg_optimizer
Routines for Geometry optimization using Conjugate Gradients
cg_utils
Utilities for Geometry optimization using Conjugate Gradients
cp_lbfgs
LBFGS-B routine (version 3.0, April 25, 2011)
cp_lbfgs_geo
Main driver for L-BFGS optimizer
cp_lbfgs_optimizer_gopt
routines that optimize a functional using the limited memory bfgs quasi-newton method. The process set up so that a master runs the real optimizer and the others help then to calculate the objective function. The arguments for the objective function are physicaly present in every processor (nedeed in the actual implementation of pao). In the future tha arguments themselves could be distributed.
dimer_methods
Contains types used for a Dimer Method calculations
dimer_types
Contains types used for a Dimer Method calculations
dimer_utils
Contains utilities for a Dimer Method calculations
free_energy_methods
Methods to perform free energy and free energy derivatives calculations
geo_opt
performs geometry optimization
glbopt_callback
Callback used by global geometry optimization schemes
gopt_f_methods
contains a functional that calculates the energy and its derivatives for the geometry optimizer
gopt_f_types
contains a functional that calculates the energy and its derivatives for the geometry optimizer
gopt_param_types
contains typo and related routines to handle parameters controlling the GEO_OPT module
helium_common
Independent helium subroutines shared with other modules
helium_interactions
Methods that handle helium-solvent and helium-helium interactions
helium_io
I/O subroutines for helium
helium_methods
Methods dealing with helium_solvent_type
helium_sampling
Methods for sampling helium variables
helium_types
Data types representing superfluid helium
helium_worm
Worm algorithm
input_cp2k_md
...
input_cp2k_restarts
Set of routines to dump the restart file of CP2K
input_cp2k_vib
builds the input structure for the VIBRATIONAL_ANALYSIS module
integrator
Provides integrator routines (velocity verlet) for all the ensemble types
integrator_utils
Provides integrator utility routines for the integrators
md_conserved_quantities
computes the conserved quantities for a given md ensemble and also kinetic energies, thermo/barostat stuff
md_ener_types
Split md_ener module from md_environment_type
md_energies
prints all energy info per timestep to the screen or to user defined output files
md_environment_types
...
md_run
Perform a molecular dynamics (MD) run using QUICKSTEP
md_util
Utilities for Molecular Dynamics
md_vel_utils
Collection of utilities for setting-up and handle velocities in MD runs
mdctrl_methods
A common interface (wrapper) for a callback into the md_run loop. Currently this is only used by the glbopt machinery, but its meant to be extended if others need to controll the md_run loop, too.
neb_io
I/O Module for Nudged Elastic Band Calculation
neb_md_utils
Module with utility to perform MD Nudged Elastic Band Calculation
neb_methods
Module performing a Nudged Elastic Band Calculation
neb_opt_utils
Module with utility to perform MD Nudged Elastic Band Calculation
neb_types
Typo for Nudged Elastic Band Calculation
neb_utils
Module with utility for Nudged Elastic Band Calculation
pint_gle
Methods to apply GLE to PI runs.
pint_io
I/O subroutines for pint_env
pint_methods
Methods to performs a path integral run
pint_normalmode
Data type and methods dealing with PI calcs in normal mode coords
pint_piglet
Methods to apply the piglet thermostat to PI runs.
pint_pile
Methods to apply a simple Lagevin thermostat to PI runs. v_new = c1*vold + SQRT(kT/m)*c2*random
pint_public
Public path integral routines that can be called from other modules
pint_staging
Data type and methods dealing with PI calcs in staging coordinates
pint_transformations
...
pint_types
...
reftraj_types
initialization of the reftraj structure used to analyse previously generated trajectories
reftraj_util
Initialize the analysis of trajectories to be done by activating the REFTRAJ ensemble
rt_propagation
Routines for the real time propagation.
shell_opt
simpar_methods
Methods for storing MD parameters type
thermal_region_types
Thermal regions type: to initialize and control the temperature of different regions
thermal_region_utils
Setup of regions with different temperature
velocity_verlet_control
Provides an interface to the velocity-verlet based integrator routines for all ensembles
vibrational_analysis
Module performing a vibrational analysis
wiener_process
Handling of the Wiener process currently employed in turn of the Langevin dynamics.