NetCDF store file format specification

Overview

This is a specification for the NetCDF 4 based store file format used by YANK.

Why NetCDF4?

All your questions answered here.

Format specification

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netcdf complex-explicit {
dimensions:
	iteration = UNLIMITED ; // (1 currently)
	replica = 13 ;
	atom = 48104 ;
	spatial = 3 ;
	scalar = 1 ;
variables:
	float positions(iteration, replica, atom, spatial) ;
		positions:units = "nm" ;
		positions:long_name = "positions[iteration][replica][atom][spatial] is position of coordinate \'spatial\' of atom \'atom\' from replica \'replica\' for iteration \'iteration\'." ;
	int states(iteration, replica) ;
		states:units = "none" ;
		states:long_name = "states[iteration][replica] is the state index (0..nstates-1) of replica \'replica\' of iteration \'iteration\'." ;
	float energies(iteration, replica, replica) ;
		energies:units = "kT" ;
		energies:long_name = "energies[iteration][replica][state] is the reduced (unitless) energy of replica \'replica\' from iteration \'iteration\' evaluated at state \'state\'." ;
	int64 proposed(iteration, replica, replica) ;
		proposed:units = "none" ;
		proposed:long_name = "proposed[iteration][i][j] is the number of proposed transitions between states i and j from iteration \'iteration-1\'." ;
	int64 accepted(iteration, replica, replica) ;
		accepted:units = "none" ;
		accepted:long_name = "accepted[iteration][i][j] is the number of proposed transitions between states i and j from iteration \'iteration-1\'." ;
	float box_vectors(iteration, replica, spatial, spatial) ;
		box_vectors:units = "nm" ;
		box_vectors:long_name = "box_vectors[iteration][replica][i][j] is dimension j of box vector i for replica \'replica\' from iteration \'iteration-1\'." ;
	float volumes(iteration, replica) ;
		volumes:units = "nm**3" ;
		volumes:long_name = "volume[iteration][replica] is the box volume for replica \'replica\' from iteration \'iteration-1\'." ;
	string timestamp(iteration) ;

// global attributes:
		:title = "Replica-exchange simulation created using ReplicaExchange class of repex.py on Sun Nov 16 22:18:46 2014" ;
		:application = "YANK" ;
		:program = "yank.py" ;
		:programVersion = "unknown" ;
		:Conventions = "YANK" ;
		:ConventionVersion = "0.1" ;

group: timings {
  variables:
  	float iteration(iteration) ;
  	float mixing(iteration) ;
  	float propagate(iteration, replica) ;
  } // group timings

group: thermodynamic_states {
  variables:
  	int64 nstates ;
  	float temperatures(replica) ;
  		temperatures:units = "K" ;
  		temperatures:long_name = "temperatures[state] is the temperature of thermodynamic state \'state\'" ;
  	string systems(replica) ;
  		systems:long_name = "systems[state] is the serialized OpenMM System corresponding to the thermodynamic state \'state\'" ;
  } // group thermodynamic_states

group: options {
  variables:
  	double collision_rate ;
  		collision_rate:type = "float" ;
  		collision_rate:units = "/picosecond" ;
  	double constraint_tolerance ;
  		constraint_tolerance:type = "float" ;
  	double timestep ;
  		timestep:type = "float" ;
  		timestep:units = "femtosecond" ;
  	int64 nsteps_per_iteration ;
  		nsteps_per_iteration:type = "int" ;
  	int64 number_of_iterations ;
  		number_of_iterations:type = "int" ;
  	double equilibration_timestep ;
  		equilibration_timestep:type = "float" ;
  		equilibration_timestep:units = "femtosecond" ;
  	int64 number_of_equilibration_iterations ;
  		number_of_equilibration_iterations:type = "int" ;
  	string title(scalar) ;
  		title:type = "str" ;
  	int64 minimize ;
  		minimize:type = "bool" ;
  	string replica_mixing_scheme(scalar) ;
  		replica_mixing_scheme:type = "str" ;
  	int64 online_analysis ;
  		online_analysis:type = "bool" ;
  	int64 verbose ;
  		verbose:type = "bool" ;
  	int64 show_mixing_statistics ;
  		show_mixing_statistics:type = "bool" ;
  	int64 mc_atoms ;
  		mc_atoms:type = "NoneType" ;
  	int64 mc_displacement ;
  		mc_displacement:type = "bool" ;
  	int64 mc_rotation ;
  		mc_rotation:type = "bool" ;
  	double displacement_sigma ;
  		displacement_sigma:type = "float" ;
  		displacement_sigma:units = "nanometer" ;
  	int64 displacement_trials_accepted ;
  		displacement_trials_accepted:type = "int" ;
  	int64 rotation_trials_accepted ;
  		rotation_trials_accepted:type = "int" ;
  } // group options

group: metadata {
  variables:
  	double standard_state_correction ;
  } // group metadata
}