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.