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.
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__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. Note that SOMD only uses a seed for FreeEnergy protocols. The seed should only be used for debugging purposes since SOMD uses the same seed for each Monte Carlo cycle.
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.
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.
Get the command-line arguments string.
Convert the argument dictionary into a list of strings.
getArgs
()Get the dictionary of command-line arguments.
Get the list of configuration file strings.
getCurrentGradient
([time_series])Get the current free energy gradient.
Get the latest molecular system.
getCurrentTime
([time_series])Get the current time (in nanoseconds).
getFrame
(index)Return a specific trajectory frame.
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.
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.
Return the list of input files.
insertArg
(arg, value, index)Insert a command-line argument at a specific index.
isError
()Return whether the process exited with an error.
isQueued
()Return whether the process is queued.
Return whether the process is running.
kill
()Kill the running process.
Reset the command-line arguments.
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.
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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.
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clearArgs
()¶ Clear all of the command-line arguments.
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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.
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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
-
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
-
getFrame
(index)¶ Return a specific trajectory frame.
- Parameters
index (int) – The index of the frame.
- Returns
frame – The System object of the corresponding frame.
- Return type
-
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
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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
output – A path, or file link, to an archive of the process input.
- Return type
str, IPython.display.FileLink
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getName
()¶ Return the process name.
Returns:
- namestr
The name of the process.
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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
output – 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
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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
-
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
-
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
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inputFiles
()¶ Return the list of input files.
- Returns
input_files – The list of autogenerated input files.
- Return type
[str]
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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 exited with an error.
- Returns
is_error – Whether the process exited with an error.
- 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
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kill
()¶ Kill the running process.
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resetArgs
()¶ Reset the command-line arguments.
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resetConfig
()¶ Reset the configuration parameters.
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run
(system=None, protocol=None, auto_start=True, restart=False)¶ Create and run a new process.
- Parameters
- Returns
process – The new process object.
- Return type
-
runTime
()¶ Return the running time for the process (in minutes).
- Returns
runtime – The runtime in minutes.
- Return type
-
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.
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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
-
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.
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wait
(max_time=None)¶ Wait for the process to finish.
- Parameters
max_time (
Time
, int, float) – The maximum time to wait (in minutes).
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workDir
()¶ Return the working directory.
- Returns
work_dir – The path of the working directory.
- Return type
str
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writeConfig
(file)¶ Write the configuration to file.
- Parameters
file (str) – The path to a file.
-