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.
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, autostart, 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

getName()

Return the process name.

Returns:

name : str
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, autostart=True, restart=False)

Create and run a new process.

Parameters:
  • system (System) – The molecular system.
  • protocol (Protocol) – The simulation protocol.
  • autostart (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.