BioSimSpace.Process.Namd¶
-
class
BioSimSpace.Process.
Namd
(system, protocol, exe=None, name='namd', work_dir=None, seed=None, property_map={})¶ A class for running simulations using NAMD.
-
__init__
(system, protocol, exe=None, name='namd', work_dir=None, seed=None, property_map={})¶ Constructor.
- Parameters
system (
System
) – The molecular system.protocol (
Protocol
) – The protocol for the NAMD process.exe (str) – The full path to the NAMD executable.
name (str) – The name of the process.
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.
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.
eta
()Get the estimated time for the process to finish (in minutes).
exe
()Return the executable.
getAngleEnergy
([time_series, block])Get the angle energy.
Get the command-line arguments string.
Convert the argument dictionary into a list of strings.
getArgs
()Get the dictionary of command-line arguments.
getBondEnergy
([time_series, block])Get the bond energy.
getBoundaryEnergy
([time_series, block])Get the boundary energy.
Get the list of configuration file strings.
getCurrentAngleEnergy
([time_series])Get the current angle energy.
getCurrentBondEnergy
([time_series])Get the current bond energy.
getCurrentBoundaryEnergy
([time_series])Get the current boundary energy.
getCurrentDihedralEnergy
([time_series])Get the current total dihedral energy (proper + improper).
getCurrentElectrostaticEnergy
([time_series])Get the current electrostatic energy.
getCurrentGPressure
([time_series])Get the current pressure.
getCurrentGPressureAverage
([time_series])Get the current average pressure.
getCurrentImproperEnergy
([time_series])Get the current improper energy.
getCurrentKineticEnergy
([time_series])Get the current kinetic energy.
getCurrentMiscEnergy
([time_series])Get the current external energy.
getCurrentPotentialEnergy
([time_series])Get the current potential energy.
getCurrentPressure
([time_series])Get the current pressure.
getCurrentPressureAverage
([time_series])Get the current average pressure.
getCurrentProperEnergy
([time_series])Get the current proper dihedral energy.
getCurrentRecord
(record[, time_series, unit])Get a current record from the stdout dictionary.
Return the current dictionary of stdout time-series records.
getCurrentStep
([time_series])Get the current number of integration steps.
Get the latest molecular system.
getCurrentTemperature
([time_series])Get the temperature.
getCurrentTemperatureAverage
([time_series])Get the current average temperature.
getCurrentTime
([time_series])Get the current simulation time.
getCurrentTotal2Energy
([time_series])Get the current total energy.
getCurrentTotal3Energy
([time_series])Get the total energy.
getCurrentTotalEnergy
([time_series])Get the current potential energy.
getCurrentVanDerWaalsEnergy
([time_series])Get the current Van der Waals energy.
getCurrentVolume
([time_series])Get the current volume.
getDihedralEnergy
([time_series, block])Get the total dihedral energy (proper + improper).
getElectrostaticEnergy
([time_series, block])Get the electrostatic energy.
getFrame
(index)Return a specific trajectory frame.
getGPressure
([time_series, block])Get the pressure.
getGPressureAverage
([time_series, block])Get the average pressure.
getImproperEnergy
([time_series, block])Get the improper energy.
getInput
([name, file_link])Return a link to a zip file containing the input files used by the process.
getKineticEnergy
([time_series, block])Get the kinetic energy.
getMiscEnergy
([time_series, block])Get the external energy.
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.
getPotentialEnergy
([time_series, block])Get the potential energy.
getPressure
([time_series, block])Get the pressure.
getPressureAverage
([time_series, block])Get the average pressure.
getProperEnergy
([time_series, block])Get the proper dihedral energy.
getRecord
(record[, time_series, unit, block])Get a record from the stdout dictionary.
getRecords
([block])Return the dictionary of stdout time-series records.
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.
getStep
([time_series, block])Get the number of integration steps.
getSystem
([block])Get the latest molecular system.
getTemperature
([time_series, block])Get the temperature.
getTemperatureAverage
([time_series, block])Get the average temperature.
getTime
([time_series, block])Get the simulation time.
getTotal2Energy
([time_series, block])Get the total energy.
getTotal3Energy
([time_series, block])Get the total energy.
getTotalEnergy
([time_series, block])Get the total energy.
getTrajectory
([block])Return a trajectory object.
getVanDerWaalsEnergy
([time_series, block])Get the Van der Vaals energy.
getVolume
([time_series, block])Get the volume.
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 NAMD 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.
-
eta
()¶ Get the estimated time for the process to finish (in minutes).
- Returns
eta – The estimated remaining time in minutes.
- Return type
-
exe
()¶ Return the executable.
- Returns
exe – The path to the executable.
- Return type
str
-
getAngleEnergy
(time_series=False, block='AUTO')¶ Get the angle energy.
- 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
energy – The angle energy.
- Return type
-
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
-
getBondEnergy
(time_series=False, block='AUTO')¶ Get the bond energy.
- 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
energy – The bond energy.
- Return type
-
getBoundaryEnergy
(time_series=False, block='AUTO')¶ Get the boundary energy.
- 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
energy – The boundary energy.
- Return type
-
getConfig
()¶ Get the list of configuration file strings.
- Returns
config – The list of configuration strings.
- Return type
[str]
-
getCurrentAngleEnergy
(time_series=False)¶ Get the current angle energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The angle energy.
- Return type
-
getCurrentBondEnergy
(time_series=False)¶ Get the current bond energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The bond energy.
- Return type
-
getCurrentBoundaryEnergy
(time_series=False)¶ Get the current boundary energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The boundary energy.
- Return type
-
getCurrentDihedralEnergy
(time_series=False)¶ Get the current total dihedral energy (proper + improper).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The dihedral energy.
- Return type
-
getCurrentElectrostaticEnergy
(time_series=False)¶ Get the current electrostatic energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The electrostatic energy.
- Return type
-
getCurrentGPressure
(time_series=False)¶ Get the current pressure. (Hydrogens incorporated into bonded atoms.).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
pressure – The pressure.
- Return type
-
getCurrentGPressureAverage
(time_series=False)¶ Get the current average pressure. (Hydrogens incorporated into bonded atoms.).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
pressure – The average pressure.
- Return type
-
getCurrentImproperEnergy
(time_series=False)¶ Get the current improper energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The improper energy.
- Return type
-
getCurrentKineticEnergy
(time_series=False)¶ Get the current kinetic energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The current kinetic energy.
- Return type
-
getCurrentMiscEnergy
(time_series=False)¶ Get the current external energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The external energy.
- Return type
-
getCurrentPotentialEnergy
(time_series=False)¶ Get the current potential energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The potential energy.
- Return type
-
getCurrentPressure
(time_series=False)¶ Get the current pressure.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
pressure – The pressure.
- Return type
-
getCurrentPressureAverage
(time_series=False)¶ Get the current average pressure.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
pressure – The average pressure.
- Return type
-
getCurrentProperEnergy
(time_series=False)¶ Get the current proper dihedral energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The proper dihedral energy.
- Return type
-
getCurrentRecord
(record, time_series=False, unit=None)¶ Get a current record from the stdout dictionary.
-
getCurrentRecords
()¶ Return the current dictionary of stdout time-series records.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
records – The dictionary of time-series records.
- Return type
BioSimSpace.Process._process._MultiDict
-
getCurrentStep
(time_series=False)¶ Get the current number of integration steps.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
step – The current number of integration steps.
- Return type
int
-
getCurrentSystem
()¶ Get the latest molecular system.
- Returns
system – The latest molecular system.
- Return type
-
getCurrentTemperature
(time_series=False)¶ Get the temperature.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
temperature – The temperature.
- Return type
-
getCurrentTemperatureAverage
(time_series=False)¶ Get the current average temperature.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
temperature – The average temperature.
- Return type
-
getCurrentTime
(time_series=False)¶ Get the current simulation time.
- 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
-
getCurrentTotal2Energy
(time_series=False)¶ Get the current total energy. (Better KE conservation.).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The total energy.
- Return type
-
getCurrentTotal3Energy
(time_series=False)¶ Get the total energy. (Smaller short-time fluctuations.).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The total energy.
- Return type
-
getCurrentTotalEnergy
(time_series=False)¶ Get the current potential energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The total energy.
- Return type
-
getCurrentVanDerWaalsEnergy
(time_series=False)¶ Get the current Van der Waals energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The Van der Vaals energy.
- Return type
-
getCurrentVolume
(time_series=False)¶ Get the current volume.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
volume – The volume.
- Return type
-
getDihedralEnergy
(time_series=False, block='AUTO')¶ Get the total dihedral energy (proper + improper).
- 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
energy – The total dihedral energy.
- Return type
-
getElectrostaticEnergy
(time_series=False, block='AUTO')¶ Get the electrostatic energy.
- 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
energy – The electrostatic energy.
- 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
-
getGPressure
(time_series=False, block='AUTO')¶ Get the pressure. (Hydrogens incorporated into bonded atoms.).
- 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
pressure – The pressure.
- Return type
-
getGPressureAverage
(time_series=False, block='AUTO')¶ Get the average pressure. (Hydrogens incorporated into bonded atoms.).
- 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
pressure – The average pressure.
- Return type
-
getImproperEnergy
(time_series=False, block='AUTO')¶ Get the improper energy.
- 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
energy – The improper energy.
- Return type
-
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
-
getKineticEnergy
(time_series=False, block='AUTO')¶ Get the kinetic energy.
- 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
energy – The kinetic energy.
- Return type
-
getMiscEnergy
(time_series=False, block='AUTO')¶ Get the external energy.
- 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
energy – The external energy.
- Return type
-
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
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
-
getPotentialEnergy
(time_series=False, block='AUTO')¶ Get the potential energy.
- 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
energy – The potential energy.
- Return type
-
getPressure
(time_series=False, block='AUTO')¶ Get the pressure.
- 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
pressure – The pressure.
- Return type
-
getPressureAverage
(time_series=False, block='AUTO')¶ Get the average pressure.
- 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
pressure – The average pressure.
- Return type
-
getProperEnergy
(time_series=False, block='AUTO')¶ Get the proper dihedral energy.
- 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
energy – The proper dihedral energy.
- Return type
-
getRecord
(record, time_series=False, unit=None, block='AUTO')¶ Get a record from the stdout dictionary.
-
getRecords
(block='AUTO')¶ Return the dictionary of stdout time-series records.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
records – The dictionary of time-series records.
- Return type
dict
-
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]
-
getStep
(time_series=False, block='AUTO')¶ Get the number of integration steps.
- 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
step – The current number of integration steps.
- Return type
int
-
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
-
getTemperature
(time_series=False, block='AUTO')¶ Get the temperature.
- 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
temperature – The temperature.
- Return type
-
getTemperatureAverage
(time_series=False, block='AUTO')¶ Get the average temperature.
- 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
temperature – The average temperature.
- Return type
-
getTime
(time_series=False, block='AUTO')¶ Get the simulation time.
- 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
-
getTotal2Energy
(time_series=False, block='AUTO')¶ Get the total energy. (Better KE conservation.).
- 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
energy – The total energy.
- Return type
-
getTotal3Energy
(time_series=False, block='AUTO')¶ Get the total energy. (Smaller short-time fluctuations.).
- 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
energy – The total energy.
- Return type
-
getTotalEnergy
(time_series=False, block='AUTO')¶ Get the total energy.
- 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
energy – The total energy.
- 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
-
getVanDerWaalsEnergy
(time_series=False, block='AUTO')¶ Get the Van der Vaals energy.
- 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
energy – The Van der Vaals energy.
- Return type
-
getVolume
(time_series=False, block='AUTO')¶ Get the volume.
- 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
volume – The volume.
- Return type
-
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 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
-
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
- 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.
-
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 NAMD process.
- Returns
process – The process object.
- 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.
-
wait
(max_time=None)¶ Wait for the process to finish.
- Parameters
max_time (
Time
, int, float) – The maximum 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.
-