Calculate Permeability¶
Calculate the permeability coefficient using the permeation rate estimated from the WE simulation data.
Calculation Parameters¶
Compartment Size Scaling Factor (compartment_size_scale) type: decimal: The scaling factor for the (donor) compartment size (i.e., (simulation box length - membrane width)/2).Default: 1.0 , Max: 2.0 CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592 GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16 Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “” Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluatedDefault: 600 , Min: 300 Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592 Metric Period (metric_period) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300 Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required Log Verbosity (verbosity) type: string: verbose levelDefault: debugChoices: info, warning, error, debug, ddebug
Field parameters¶
Box Edges Field (box_edges_field) type: Field Type: FloatVec: Field containing the solvated molecule and the membrane.Default: Box Edges Compartment Size Field (compartment_size_field) type: Field Type: Float: Field containing the size of the donor compartment.Default: Compartment Size Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field None (in_mol_field) type: Field Type: Chem.Mol: Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field Log Estimated Permeability Evolution Field (permeabilities_field) type: Field Type: NumPy.NDArray: Field containing the evolution of permeability estimates and their confidence interval (upper and lower bounds) in log-scale.Default: Log Estimated Permeability Evolution Log Estimated Permeability Field (permeability_field) type: Field Type: FloatVec: Field containing the final permeability estimates and their confidence interval (upper and lower bounds) in log-scale.Default: Log Estimated Permeability Rates Field (rates_field) type: Field Type: NumPy.NDArray: Field containing the calculated rates.Default: Rates Log Estimated Permeability Evolution Field (red_permeabilities_field) type: Field Type: NumPy.NDArray: Field containing the evolution of permeability estimates and their confidence interval (upper and lower bounds) in log-scale.Default: Log Estimated Permeability Evolution Log Estimated Permeability Field (red_permeability_field) type: Field Type: FloatVec: Field containing the final permeability estimates and their confidence interval (upper and lower bounds) in log-scale.Default: Log Estimated Permeability Rates Field (red_rates_field) type: Field Type: NumPy.NDArray: Field containing the calculated rates.Default: Rates
Hardware Parameters¶
- Machine hardware requirements
- Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592
- Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64
- Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32
- Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluatedDefault: 600 , Min: 300
- Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592
- GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128
- Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
- Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
- Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “”
Metrics Parameters¶
- Cube Metric Parameters
- Metric Period (None) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network