- Generated by
1.9.8
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RASPA3 3.0.13
A molecular simulation code for computing adsorption and diffusion in nanoporous materials
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"SimulationType" : "MonteCarlo" Starts the Monte Carlo part of RASPA. The particular ensemble is not specified but implicitly deduced from the specified Monte Carlo moves. Note that a MD-move can be used for hybrid MC/MD."SimulationType" : "MolecularDynamics" Starts the Molecular Dynamics part of RASPA. The ensemble must be explicitly specified."NumberOfCycles" : integer The number of cycles for the production run. For Monte Carlo a cycle consists of $N$ steps, where $N$ is the amount of molecules with a minimum of 20 steps. This means that on average during each cycle on each molecule a Monte Carlo move has been attempted (either successful or unsuccessful). For MD the number of cycles is simply the amount of integration steps."NumberOfInitializationCycles": integer The number of cycles used to initialize the system using Monte Carlo. This can be used for both Monte Carlo as well as Molecular Dynamics to quickly minimize the positions of the atoms in the system."NumberOfEquilibrationCycles" : integer For Molecular Dynamics it is the number of MD steps to equilibrate the velocities in the systems. After this equilibration the production run is started. For Monte Carlo, in particular CFCMC, the equilibration-phase is used to measure the biasing factors, using Wang-Landau estimation."RestartFile" : boolean Reads the positions, velocities, and force from the directory 'RestartInitial'. Any creation of molecules in the 'simulation.input' file will be in addition and after this first read from file. This is useful to load initial positions of cations for example, and after that create adsorbates. The restart file is written at 'PrintEvery' intervals."ContinueAfterCrash" : boolean Write a binary file containing the complete status of the program. The file name is 'restart_data.bin'. With this option to true the presence of this file will result in continuation from the point where the program was at the moment of outputting this file. The file can be quite big (several hundreds of megabytes) and will be outputted every 'WriteBinaryRestartFileEvery' cycles."WriteBinaryRestartFileEvery" : integer The output frequency (i.e. every int cycles) of writing the crash-recovery file."PrintEvery" : integer Prints the loadings (when a framework is present) and energies every int cycles. For MD information like energy conservation and stress are printed."RescaleWangLandauEvery" : integer Determines the frequency of updates for optimizing the λ parameter in for example Continuous Fractional Component Monte Carlo during the equilibration phase of the simulation."OptimizeMCMovesEvery" : integer Determines the frequency of updating the maximum change in the Monte Carlo moves towards an optimal acceptance ratio (default: 0.5). For Translation, the maximum displacement is optimized, for rotation the maximum angle, for hybrid MC the maximum timestep etc."Systems" : list List of system settings, each containing a dictionary with possible key-value pairs described below. Multiple systems can be owned by one process and Monte Carlo moves starting with Gibbs and parallel tempering act on two systems."Components" : list List of component settings, each containing a dictionary with possible key-value pairs described below."ExternalTemperature" : floating-point-number The external temperature in Kelvin for the system. From this, the system beta is calculated, which is central in all statistics. Default: 298"ExternalPressure" : floating-point-number The external pressure in Pascal for the system. Default: 0"ThermostatChainLength" : integer The length of the chain to thermostat the system. Default: 5"NumberOfYoshidaSuzukiSteps" : integer The number of Yoshida/Suzuki multiple timesteps. Default: 5"TimeScaleParameterThermostat" : floating-point-number The time scale on which the system thermostat evolves. Default: 0.15"Type" : string Sets the system type. The type string can be:"Box" Sets the system to a simulation cell where the lengths and angles of the cell can be explicitely be specified."Framework" Set the system to type 'Framework'. The cell lengths and cell angles follows from the specified framework file."BoxLengths" : [floating-point-number, floating-point-number, floating-point-number] The cell dimensions of rectangular box of system in Angstroms."BoxAngles" : [floating-point-number, floating-point-number, floating-point-number] The cell angles of rectangular box of system in Degrees."Name" : string For "Type" : "Framework", loads the framework with filename string.cif."NumberOfUnitCells" : [integer, integer, integer] The number of unit cells in x, y, and z direction for the system. The super-cell will contain the unit cells, and periodic boundary conditions will be applied on the super-cell level (not on a unit cell level)."HeliumVoidFraction" : floating-point-number Sets the void fraction as measured by probing the structure with helium a room temperature. This quantity has to be obtained from a separate simulation and is essential to compute the excess-adsorption during the simulation."UseChargesFrom" : string Specifies the way to define the framework charges. The string can be:"PseudoAtoms" Takes the charges from the force-field definition file."CIF_File" Takes the charges from the definitions in the CIF-file. The charges for the atoms list in the file needs to be given using the _atom_site_charge tag. Using this option allows for individual charges for each framework atom, even when having the same atom-type."ChargeEquilibration" Computes the framework charges uses the charge equilibration scheme of Wilmer and Snurr. The charges are symmetrized over the asymmetric atoms."ForceField" : string Reads in the force field file string.json, Note that if this file is in the working directory then this will be read and used instead of: ${RASPA_DIR}/simulations/share/raspa3/forcefield/string/force_field.json
"CutOffFrameworkVDW" : floating-point-number The cutoff of the Van der Waals potentials for framework-molecule interactions. Interactions longer then this distance are omitted from the energy and force computations."CutOffMoleculeVDW" : floating-point-number The cutoff of the Van der Waals potentials for molecule-molecule interactions. Interactions longer then this distance are omitted from the energy and force computations."CutOffVDW" : floating-point-number The cutoff of the Van der Waals potentials. Interactions longer then this distance are omitted from the energy and force computations. The option CutOffVDW implies setting both CutOffFrameworkVDW and CutOffMoleculeVDW."CutOffCoulombic" : floating-point-number The cutoff of the charge-charge potential. The potential is truncated at the cutoff. No tail-corrections are (or can be) applied. The only way to include the long-range part is to use 'ChargeMethod Ewald'. The parameter is also used in combination with the Ewald precision to compute the number of wave vectors and Ewald parameter $\alpha$. For the Ewald summation using rather large unit cells, a charge-charge cutoff of about half the smallest box-length would be advisable in order to avoid the use of an excessive amount of wave-vectors in Fourier space. For non-Ewald methods the cutoff should be as large as possible (greater than about 30 Å)."CutOff" : floating-point-number Implies setting CutOffFrameworkVDW, CutOffMoleculeVDW, and CutOffCoulomb"ChargeMethod" : string Sets the method to compute charges. The string can be:"None" Skips the entire charge calculation and should only be used when all adsorbates do not contain any charges."Ewald" Switches on the Ewald summation for the charge calculation.MC-moves"VolumeChangeProbability" : floating-point-number The probability per cycle to attempt a volume-change. Rigid molecules are scaled by center-of-mass, while flexible molecules and the framework is atomically scaled."GibbVolumeChangeProbability" : floating-point-number The probability per cycle to attempt a Gibbs volume-change MC move during a Gibbs ensemble simulation. The total volume of the two boxes (usually one for the gas phase, one for the liquid phase) remains constant, but the individual volume of the boxes are changed. The volumes are changed by a random change in $\ln(V_I/V_{II})$."GibbVolumeChangeProbability" : floating-point-number The probability per cycle to attempt a Hybrid MC move. A hybrid MC move propagates the Hamiltonian via a short Molecular Dynamics simulation and accepts the new state based on the drift."TimeStep" : floating-point-number The time step in picoseconds for MD integration. Default value: 0.0005"Ensemble" : string Sets the ensemble. The ensemble string can be:"NVE"\ The micro canonical ensemble, the number of particle $N$, the volume $V$, and the energy $E$ are constant."NVT"\ The canonical ensemble, the number of particle $N$, the volume $V$, and the average temperature $\left\langle T\right\rangle$ are constant. Instantaneous values for the temperature are fluctuating."OutputPDBMovie" : boolean
Sets whether or not to output simulation snapshots to pdb movies. Output is written to the directory movies.
"SampleMovieEvery" : integer Sample the movie every int cycles. Default: 1"ComputeEnergyHistogram" : boolean
Sets whether or not to compute a histogram of the energy for the current system. For example, during adsorption it keeps track of the total energy, the VDW energy, the Coulombic energy, and the polarization energy.\ Output is written to the directory energy_histogram.
"SampleEnergyHistogramEvery" : integer Sample the energy histogram of the system every int cycles. Default: 1"WriteEnergyHistogramEvery" : integer Writes the energy histogram of the system every int cycles. Default: 5000"NumberOfBinsEnergyHistogram" : integer Sets the number of elements of the histogram. Default: 128"LowerLimitEnergyHistogram" : floating-point-number The lower limit of the histogram. Default: -5000"UpperLimitEnergyHistogram" : floating-point-number The upper limit of the histogram. Default: 1000"ComputeNumberOfMoleculesHistogram" : boolean
Sets whether or not to compute the histograms of the number of molecules for the current system. In open ensembles the number of molecules fluctuates.\ Output is written to the directory number_of_molecules_histogram.
"SampleNumberOfMoleculesHistogramEvery" : integer Sample the histogram every int cycles. Default: 1"WriteNumberOfMoleculesHistogramEvery" : integer Output the histogram every int cycles. Default: 5000"LowerLimitNumberOfMoleculesHistogram" : floating-point-number The lower limit of the histograms. Default: 0"UpperLimitNumberOfMoleculesHistogram" : floating-point-number The upper limit of the histograms. Default: 200"ComputeRDF" : boolean
Sets whether or not to compute the radial distribution function (RDF).\ Output is written to the directory rdf.
"SampleRDFEvery" : integer Sample the rdf every int cycles. Default: 10"WriteRDFEvery" : integer Output the rdf every int cycles. Default: 5000"NumberOfBinsRDF" : integer Sets the number of elements of the rdf. Default: 128"UpperLimitRDF" : floating-point-number The upper limit of the rdf. Default: 15.0"ComputeConventionalRDF" : boolean
Sets whether or not to compute the radial distribution function (RDF). Output is written to the directory conventional_rdf.
"SampleConventionalRDFEvery" : integer Sample the rdf every int cycles. Default: 10"WriteConventionalRDFEvery" : integer Output the rdf every int cycles. Default: 5000"NumberOfBinsConventionalRDF" : integer Sets the number of elements of the rdf. Default: 128"UpperLimitConventionalRDF" : floating-point-number The upper limit of the rdf. Default: 15.0"ComputeMSD" : boolean
Sets whether or not to compute the mean-squared displacement (MSD). Output is written to the directory msd.
"SampleMSDEvery" : integer Sample the msd every int cycles. Default: 10"WriteMSDEvery" : integer Output the msd every int cycles. Default: 5000"NumberOfBlockElementsMSD" : integer The number of elements per block of the msd. Default: 25.0"ComputeDensityGrid" : boolean
Sets whether or not to compute the density grids. Output is written to the directory density_grids.
"SampleDensityGridEvery" : integer Sample the density grids every int cycles. Default: 10"WriteDensityGridEvery" : integer Output the density grids every int cycles. Default: 5000"DensityGridSize" : [integer, integer, integer] Sets the size of the density grids. Default: [128, 128, 128]"Name" : string The descriptive name of the component."MolFraction" : floating-point-number The mol fraction of this component in the mixture. The values can be specified relative to other components, as the fractions are normalized afterwards. The partial pressures for each component are computed from the total pressure and the mol fraction per component."FugacityCoefficient" : floating-point-number The fugacity coefficient for the current component. For values 0 (or by not specifying this line), the fugacity coefficients are automatically computed using the Peng-Robinson equation of state. Note the critical pressure, critical temperature, and acentric factor need to be specified in the molecule file."IdealGasRosenbluthWeight" : floating-point-number The ideal Rosenbluth weight is the growth factor of the CBMC algorithm for a single chain in an empty box. The value only depends on temperature and therefore needs to be computed only once. For adsorption, specifying the value in advance is convenient because the applied pressure does not need to be corrected afterwards (the Rosenbluth weight corresponds to a shift in the chemical potential reference value, and the chemical potential is directly obtained from the fugacity). For equimolar mixtures this is essential."CreateNumberOfMolecules" : integer The number of molecule to create for the current component. Note these molecules are in addition to anything read in by using a restart-file. Usually, when the restart-file is used the amount here should be put back to zero. A warning, putting this value unreasonably high results in an infinite loop. The routine accepts molecules that are grown causing no overlap (energy smaller than 'EnergyOverlapCriteria'). Also the initial starting configurations are far from optimal and substantial equilibration is needed to reduce the energy. However, the CBMC growth is able to reach very high densities."BlockingPockets" : [[3 x floating-point-number, floating-point-number]] Block certain pockets in the simulation volume. The growth of a molecule is not allowed in a blocked pocket. A typical example is the sodalite cages in FAU and LTA-type zeolites, these are not accessible to molecules like methane and bigger. The pockets are specified as a list of 4 floating points numbers: the $s_x$, $s_y$, $s_z$ fractional positions and a radius in Angstrom.
For example, blocking pockets for ITQ-29 for small molecules are specified as:
"BlockingPockets" : [
[0.0, 0.0, 0.0, 4.0],
[0.5, 0.0, 0.0, 0.5],
[0.0, 0.5, 0.0, 0.5],
[0.0, 0.0, 0.5, 0.5]
]
"LambdaBiasFileName" : string Pointing this parameter to a json file containing preset λ values allows optimized CFCMC simulations to be run without Wang-Landau estimation of the biasing weights."ThermodynamicIntegration" : boolean Boolean switch to determine whether to do a thermodynamic integration over dU/dλ for the fractional component.MC**-moves"TranslationProbability" : floating-point-number The relative probability to attempt a translation move for the current component. A random displacement is chosen in the allowed directions (see 'TranslationDirection'). Note that the internal configuration of the molecule is unchanged by this move. The maximum displacement is scaled during the simulation to achieve an acceptance ratio of 50%."RandomTranslationProbability" : floating-point-number The relative probability to attempt a random translation move for the current component. The displacement is chosen such that any position in the box can reached. It is therefore similar as reinsertion, but 'reinsertion' changes the internal conformation of a molecule and uses biasing."RotationProbability" : floating-point-number The relative probability to attempt a random rotation move for the current component. The rotation is around the starting bead. A random vector on a sphere is generated, and the rotation is random around this vector."ReinsertionProbability" : floating-point-number The relative probability to attempt a full reinsertion move for the current component. Multiple first beads are chosen, and one of these is selected according to its Boltzmann weight. The remaining part of the molecule is grown using biasing. This move is very useful, and often necessary, to change the internal configuration of flexible molecules."SwapConventionalProbability" : floating-point-number The relative probability to attempt a insertion or deletion move. Whether to insert or delete is decided randomly with a probability of 50% for each. The swap move imposes a chemical equilibrium between the system and an imaginary particle reservoir for the current component."SwapProbability" : floating-point-number The relative probability to attempt a insertion or deletion move using CBMC. Whether to insert or delete is decided randomly with a probability of 50% for each. The swap move imposes a chemical equilibrium between the system and an imaginary particle reservoir for the current component. The move starts with multiple first bead, and grows the remainder of the molecule using biasing."CFCMC_SwapProbability" : floating-point-number The relative probability to attempt a insertion or deletion move via CFCMC scheme."CFCMC_CBMC_SwapProbability" : floating-point-number The relative probability to attempt a insertion or deletion move via CB/CFCMC scheme.GibbsSwapProbability" : floating-point-number</tt>
The relative probability to attempt a Gibbs swap MC move for the
current component. The 'GibbsSwapMove' transfers a randomly selected
particle from one box to the other (50% probability to transfer a
particle from box <tt>I</tt> to <tt>II</tt>, an 50% visa versa).
- <tt>Gibbs_CFCMC_SwapProbability" : floating-point-number The relative probability to attempt a Gibbs swap MC move for the current component using the CFCMC scheme."WidomProbability" : floating-point-number The relative probability to attempt a Widom particle insertion move for the current component. The Widom particle insertion moves measure the chemical potential and can be directly related to Henry coefficients and heats of adsorption. 1.9.8