BioSimSpace.Process.Somd

class BioSimSpace.Process.Somd(system, protocol, exe=None, name='somd', platform='CPU', work_dir=None, seed=None, property_map={})

A class for running simulations using SOMD.

__init__(system, protocol, exe=None, name='somd', platform='CPU', work_dir=None, seed=None, property_map={})

Constructor.

Parameters
  • system (System) – The molecular system.

  • protocol (Protocol) – The protocol for the SOMD process.

  • exe (str) – The full path to the SOMD executable.

  • name (str) – The name of the process.

  • platform (str) – The platform for the simulation: “CPU”, “CUDA”, or “OPENCL”.

  • work_dir – The working directory for the process.

  • seed (int) – A random number seed.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Methods

__init__(system, protocol[, exe, name, …])

Constructor.

addArgs(args)

Append additional command-line arguments.

addToConfig(config)

Add a string to the configuration list.

clearArgs()

Clear all of the command-line arguments.

command()

Return the command-line string used to run the process.

deleteArg(arg)

Delete an argument from the dictionary.

exe()

Return the executable.

getArgString()

Get the command-line arguments string.

getArgStringList()

Convert the argument dictionary into a list of strings.

getArgs()

Get the dictionary of command-line arguments.

getConfig()

Get the list of configuration file strings.

getCurrentGradient([time_series])

Get the current free energy gradient.

getCurrentSystem()

Get the latest molecular system.

getCurrentTime([time_series])

Get the current time (in nanoseconds).

getGradient([time_series, block])

Get the free energy gradient.

getInput([name, file_link])

Return a link to a zip file containing the input files used by the process.

getName()

Return the process name.

getOutput([name, block, file_link])

Return a link to a zip file of the working directory.

getPackageName()

Return the package name.

getSeed()

Return the random number seed.

getStderr([block])

Return the entire stderr for the process as a list of strings.

getStdout([block])

Return the entire stdout for the process as a list of strings.

getSystem([block])

Get the latest molecular system.

getTime([time_series, block])

Get the time (in nanoseconds).

getTrajectory([block])

Return a trajectory object.

inputFiles()

Return the list of input files.

insertArg(arg, value, index)

Insert a command-line argument at a specific index.

isError()

Return whether the process errored.

isQueued()

Return whether the process is queued.

isRunning()

Return whether the process is running.

kill()

Kill the running process.

resetArgs()

Reset the command-line arguments.

resetConfig()

Reset the configuration parameters.

run([system, protocol, auto_start, restart])

Create and run a new process.

runTime()

Return the running time for the process (in minutes).

setArg(arg, value)

Set a specific command-line argument.

setArgs(args)

Set the dictionary of command-line arguments.

setConfig(config)

Set the list of configuration file strings.

setName(name)

Set the process name.

setSeed(seed)

Set the random number seed.

start()

Start the SOMD process.

stderr([n])

Print the last n lines of the stderr buffer.

stdout([n])

Print the last n lines of the stdout buffer.

wait([max_time])

Wait for the process to finish.

workDir()

Return the working directory.

writeConfig(file)

Write the configuration to file.

addArgs(args)

Append additional command-line arguments.

Parameters

args (dict, collections.OrderedDict) – A dictionary of command line arguments.

addToConfig(config)

Add a string to the configuration list.

Parameters

config (str, [ str ]) – A configuration string, a list of configuration strings, or a path to a configuration file.

clearArgs()

Clear all of the command-line arguments.

command()

Return the command-line string used to run the process.

Returns

command – The command string.

Return type

str

deleteArg(arg)

Delete an argument from the dictionary.

Parameters

arg (str) – The argument to delete.

exe()

Return the executable.

Returns

exe – The path to the executable.

Return type

str

getArgString()

Get the command-line arguments string.

Returns

arg_string – The command-line argument string.

Return type

str

getArgStringList()

Convert the argument dictionary into a list of strings.

Returns

arg_string_list – The list of command-line arguments.

Return type

[str]

getArgs()

Get the dictionary of command-line arguments.

Returns

args – The dictionary of command-line arguments.

Return type

collections.OrderedDict

getConfig()

Get the list of configuration file strings.

Returns

config – The list of configuration strings.

Return type

[str]

getCurrentGradient(time_series=False)

Get the current free energy gradient.

Parameters

time_series (bool) – Whether to return a list of time series records.

Returns

gradient – The current free energy gradient.

Return type

float

getCurrentSystem()

Get the latest molecular system.

Returns

system – The latest molecular system.

Return type

System

getCurrentTime(time_series=False)

Get the current time (in nanoseconds).

Parameters

time_series (bool) – Whether to return a list of time series records.

Returns

time – The current simulation time in nanoseconds.

Return type

Time

getGradient(time_series=False, block='AUTO')

Get the free energy gradient.

Parameters
  • time_series (bool) – Whether to return a list of time series records.

  • block (bool) – Whether to block until the process has finished running.

Returns

gradient – The free energy gradient.

Return type

float

getInput(name=None, file_link=False)

Return a link to a zip file containing the input files used by the process.

Parameters
  • name (str) – The name of the zip file.

  • file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns

ouput – A path, or file link, to an archive of the process input.

Return type

str, IPython.display.FileLink

getName()

Return the process name.

Returns:

namestr

The name of the process.

getOutput(name=None, block='AUTO', file_link=False)

Return a link to a zip file of the working directory.

Parameters
  • name (str) – The name of the zip file.

  • block (bool) – Whether to block until the process has finished running.

  • file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns

ouput – A path, or file link, to an archive of the process output.

Return type

str, IPython.display.FileLink

getPackageName()

Return the package name.

Returns

name – The name of the package.

Return type

str

getSeed()

Return the random number seed.

Returns

seed – The random number seed.

Return type

int

getStderr(block='AUTO')

Return the entire stderr for the process as a list of strings.

Parameters

block (bool) – Whether to block until the process has finished running.

Returns

error – The list of stderror strings.

Return type

[str]

getStdout(block='AUTO')

Return the entire stdout for the process as a list of strings.

Parameters

block (bool) – Whether to block until the process has finished running.

Returns

output – The list of stdout strings.

Return type

[str]

getSystem(block='AUTO')

Get the latest molecular system.

Parameters

block (bool) – Whether to block until the process has finished running.

Returns

system – The latest molecular system.

Return type

System

getTime(time_series=False, block='AUTO')

Get the time (in nanoseconds).

Parameters
  • time_series (bool) – Whether to return a list of time series records.

  • block (bool) – Whether to block until the process has finished running.

Returns

time – The current simulation time in nanoseconds.

Return type

Time

getTrajectory(block='AUTO')

Return a trajectory object.

Parameters

block (bool) – Whether to block until the process has finished running.

Returns

trajectory – The latest trajectory object.

Return type

Trajectory

inputFiles()

Return the list of input files.

Returns

input_files – The list of autogenerated input files.

Return type

[str]

insertArg(arg, value, index)

Insert a command-line argument at a specific index.

Parameters
  • arg (str) – The argument to set.

  • value – The value of the argument.

  • index (int) – The index in the dictionary.

isError()

Return whether the process errored.

Returns

is_error – Whether the process errored.

Return type

bool

isQueued()

Return whether the process is queued.

Returns

is_queued – Whether the process is queued.

Return type

bool

isRunning()

Return whether the process is running.

Returns

is_running – Whether the process is running.

Return type

bool

kill()

Kill the running process.

resetArgs()

Reset the command-line arguments.

resetConfig()

Reset the configuration parameters.

run(system=None, protocol=None, auto_start=True, restart=False)

Create and run a new process.

Parameters
  • system (System) – The molecular system.

  • protocol (Protocol) – The simulation protocol.

  • auto_start (bool) – Whether to start the process automatically.

  • restart (bool) – Whether to restart the simulation, i.e. use the original system.

Returns

process – The new process object.

Return type

Procees

runTime()

Return the running time for the process (in minutes).

Returns

runtime – The runtime in minutes.

Return type

Time

setArg(arg, value)

Set a specific command-line argument.

For command-line flags, i.e. boolean arguments, the key should specify whether the flag is enabled (True) or not (False).

Parameters
  • arg (str) – The argument to set.

  • value (bool, str) – The value of the argument.

setArgs(args)

Set the dictionary of command-line arguments.

Parameters

args (dict, collections.OrderedDict) – A dictionary of command-line arguments.

setConfig(config)

Set the list of configuration file strings.

Parameters

config (str, [str]) – The list of configuration strings, or a path to a configuration file.

setName(name)

Set the process name.

Parameters

name (str) – The process name.

setSeed(seed)

Set the random number seed.

Parameters

seed (int) – The random number seed.

start()

Start the SOMD process.

Returns

process – A handle to the running process.

Return type

Process.Somd

stderr(n=10)

Print the last n lines of the stderr buffer.

Parameters

n (int) – The number of lines to print.

stdout(n=10)

Print the last n lines of the stdout buffer.

Parameters

n (int) – The number of lines to print.

wait(max_time=None)

Wait for the process to finish.

Parameters

max_time (Time, int, float) – The maximimum time to wait (in minutes).

workDir()

Return the working directory.

Returns

work_dir – The path of the working directory.

Return type

str

writeConfig(file)

Write the configuration to file.

Parameters

file (str) – The path to a file.