meld.vault

class meld.vault.DataStore(n_atoms, n_replicas, pdb_writer, block_size=100)

Class to handle storing data from MELD runs.

Parameters:

• n_atoms – number of atoms
• n_replicas – number of replicas
• block_size – size of netcdf blocks and frequency to do backups

Data will be stored in the ‘Data’ subdirectory. Backups will be stored in ‘Data/Backup’.

Some information is stored as python pickled files:

• data_store.dat – the DataStore object
• communicator.dat – the MPICommunicator object
• remd_runner.dat – the MasterReplicaExchangeRunner object

Other data (positions, velocities, etc) is stored in the results.nc file.

backup(stage)

Backup all files to Data/Backup.

Parameters:stage – int stage

Backup will occur if stage % backup_freq == 0

close()

Close the DataStore

initialize(mode)

Prepare to use the DataStore object.

Parameters:mode – mode to open in.

Available modes are:

• ‘w’ – create a new directory structure and initialize the hd5 file
• ‘a’ – append to the existing files
• ‘r’ – open the file in read-only mode

iterate_permutation_vectors(start=None, end=None)

Iterate over the permutation vectors from disk.

iterate_positions(start=None, end=None)

Iterate over the positions from disk.

load_acceptance_probabilities(stage)

Load acceptance probability vector from disk.

Parameters:stage – int stage to load Returns:n_replica_pairs array of int

load_all_acceptance_probabilities()

Load all acceptance probabilities from disk

Warning, this might take a lot of memory

load_all_alphas()

Load all alphas from disk.

Warning, this could use a lot of memory.

load_all_energies()

Load all energies from disk.

Warning, this could use a lot of memory

load_all_permutation_vectors()

Load all permutation vector from disk.

Warning, this might take a lot of memory

load_all_positions()

Load all positions from disk.

Warning, this could use a lot of memory.

load_all_velocities()

Load all velocities from disk.

Warning, this could use a lot of memory.

load_alphas(stage)

Load alphas from disk.

Parameters:stage – int stage to load from disk Returns:n_replicas array

load_communicator()

Load the communicator from disk

classmethod load_data_store(load_backup=False)

Load the DataStore object from disk.

load_energies(stage)

Load energies from disk.

Parameters:stage – int stage to load Returns:n_replicas array

load_permutation_vector(stage)

Load permutation vector from disk.

Parameters:stage – int stage to load Returns:n_replicas array of int

load_positions(stage)

Load positions from disk.

Parameters:stage – int stage to load

load_positions_random_access(stage)

Load positions from disk.

Parameters:stage – int stage to load

This differs from load_positions() in that you can positions from any stage, while load_positions() can only move forward in time. However, this comes at a performance penalty.

load_remd_runner()

Load replica runner from disk

load_states(stage)

Load states from disk

Parameters:stage – integer stage to load Returns:list of SystemState objects

load_velocities(stage)

Load velocities from disk.

Parameters:stage – int stage to load

save_acceptance_probabilities(accept_probs, stage)

Save acceptance probabilities vector to disk.

Parameters:

• accept_probs – n_replicas array of int
• stage – int stage to store

save_alphas(alphas, stage)

Save alphas to disk.

Parameters:

• alphas – n_replicas array
• stage – int stage to store

save_communicator(comm)

Save the communicator to disk

save_data_store()

Save this object to disk.

save_energies(energies, stage)

Save energies to disk.

Parameters:

• energies – n_replicas array
• stage – int stage to save

save_permutation_vector(perm_vec, stage)

Save permutation vector to disk.

Parameters:

• perm_vec – n_replicas array of int
• stage – int stage to store

save_positions(positions, stage)

Save the positions to disk.

Parameters:

• positions – n_replicas x n_atoms x 3 array
• stage – int stage to store

save_remd_runner(runner)

Save replica runner to disk

save_states(states, stage)

Save states to disk.

Parameters:

• states – list of SystemStage objects to store
• stage – int stage to store

save_velocities(velocities, stage)

Save velocities to disk.

Parameters:

• velocities – n_replicas x n_atoms x 3 array
• stage – int stage to store