def help(name):
"""Print the help message for the named node.
Parameters
----------
name : str
The name of the node.
"""
if type(name) is not str:
raise TypeError("'name' must be of type 'str'.")
# Apped the node directory name.
full_name = _node_dir + "/" + name
# Make sure the node exists.
if not _os.path.isfile(full_name):
if not _os.path.isfile(full_name + ".py"):
raise ValueError("Cannot find node: '%s'. " % name +
"Run 'Node.list()' to see available nodes!")
else:
full_name += ".py"
# Create the command.
command = "%s/python %s --help" % (_SireBase.getBinDir(), full_name)
# Run the node as a subprocess.
proc = _subprocess.run(command, shell=True)
def __init__(self,
system,
protocol,
exe=None,
name="somd",
platform="CPU",
work_dir=None,
seed=None,
property_map={}):
"""Constructor.
Parameters
----------
system : :class:`System <BioSimSpace._SireWrappers.System>`
The molecular system.
protocol : :class:`Protocol <BioSimSpace.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" }
"""
# Call the base class constructor.
super().__init__(system, protocol, name, work_dir, seed, property_map)
# Set the package name.
self._package_name = "SOMD"
# This process can generate trajectory data.
self._has_trajectory = True
if type(platform) is not str:
raise TypeError("'platform' must be of type 'str'.")
else:
# Strip all whitespace and convert to upper case.
platform = platform.replace(" ", "").upper()
# Check for platform support.
if platform not in self._platforms:
raise ValueError("Supported platforms are: %s" %
self._platforms.keys())
else:
self._platform = self._platforms[platform]
# If the path to the executable wasn't specified, then use the bundled SOMD
# executable.
if exe is None:
# Generate the name of the SOMD exe.
if _sys.platform != "win32":
somd_path = _SireBase.getBinDir()
somd_suffix = ""
else:
somd_path = _os.path.join(
_os.path.normpath(_SireBase.getShareDir()), "scripts")
somd_interpreter = _os.path.join(
_os.path.normpath(_SireBase.getBinDir()),
"sire_python.exe")
somd_suffix = ".py"
if type(self._protocol) is _Protocol.FreeEnergy:
somd_exe = "somd-freenrg"
else:
somd_exe = "somd"
somd_exe = _os.path.join(somd_path, somd_exe) + somd_suffix
if not _os.path.isfile(somd_exe):
raise _MissingSoftwareError(
"'Cannot find SOMD executable in expected location: '%s'" %
somd_exe)
if _sys.platform != "win32":
self._exe = somd_exe
else:
self._exe = somd_interpreter
self._script = somd_exe
else:
# Make sure executable exists.
if _os.path.isfile(exe):
self._exe = exe
else:
raise IOError("SOMD executable doesn't exist: '%s'" % exe)
# The names of the input files.
self._rst_file = "%s/%s.rst7" % (self._work_dir, name)
self._top_file = "%s/%s.prm7" % (self._work_dir, name)
# The name of the trajectory file.
self._traj_file = "%s/traj000000001.dcd" % self._work_dir
# The name of the binary restart file.
self._restart_file = "%s/latest.rst" % self._work_dir
# Set the path for the SOMD configuration file.
self._config_file = "%s/%s.cfg" % (self._work_dir, name)
# Set the path for the perturbation file.
self._pert_file = "%s/%s.pert" % (self._work_dir, name)
# Set the path for the gradient file and create the gradient list.
self._gradient_file = "%s/gradients.dat" % self._work_dir
self._gradients = []
# Create the list of input files.
self._input_files = [self._config_file, self._rst_file, self._top_file]
# Initalise the number of moves per cycle.
self._num_moves = 10000
# Initialise the buffering frequency.
self._buffer_freq = 0
# Now set up the working directory for the process.
self._setup()
.absoluteFilePath()
except:
pass
if _gmx_exe is None:
# The user has not told us where it is, so need to look in $PATH.
try:
_gmx_exe = _SireBase.findExe("gmx").absoluteFilePath()
except:
try:
_gmx_exe = _SireBase.findExe("gmx_mpi").absoluteFilePath()
except:
pass
# Set the bundled GROMACS topology file directory.
_gromacs_path = _path.dirname(_SireBase.getBinDir()) + "/share/gromacs/top"
del _environ
del _SireBase
if not _path.isdir(_gromacs_path):
_gromacs_path = None
# Try using the GROMACS exe to get the location of the data directory.
if _gmx_exe is not None:
import subprocess as _subprocess
# Generate the shell command.
_command = "%s -h 2>&1 | grep 'Data prefix' | awk -F ':' '{print $2}'" % _gmx_exe
# Run the command.
def run(name, args={}):
"""Run a node.
Parameters
----------
name : str
The name of the node.
args : dict
A dictionary of arguments to be passed to the node.
Returns
-------
output : dict
A dictionary containing the output of the node.
"""
# Validate the input.
if type(name) is not str:
raise TypeError("'name' must be of type 'str'.")
if type(args) is not dict:
raise TypeError("'args' must be of type 'dict'.")
# Apped the node directory name.
full_name = _node_dir + "/" + name
# Make sure the node exists.
if not _os.path.isfile(full_name):
if not _os.path.isfile(full_name + ".py"):
raise ValueError("Cannot find node: '%s'. " % name +
"Run 'Node.list()' to see available nodes!")
else:
full_name += ".py"
# Write a YAML configuration file for the BioSimSpace node.
if len(args) > 0:
with open("input.yaml", "w") as file:
_yaml.dump(args, file, default_flow_style=False)
# Create the command.
command = "%s/python %s --config input.yaml" % (_SireBase.getBinDir(),
full_name)
# No arguments.
else:
command = "%s/python %s" % (_SireBase.getBinDir(), full_name)
# Run the node as a subprocess.
proc = _subprocess.run(command, shell=True)
if proc.returncode == 0:
# Read the output YAML file into a dictionary.
with open("output.yaml", "r") as file:
output = _yaml.safe_load(file)
# Delete the redundant YAML files.
_os.remove("input.yaml")
_os.remove("output.yaml")
return output
def _find_md_package(system, protocol, gpu_support=False):
"""Find a molecular dynamics package on the system and return
a handle to it as a MDPackage object.
Parameters
----------
system : :class:`System <BioSimSpace._SireWrappers.System>`
The molecular system.
protocol : :class:`Protocol <BioSimSpace.Protocol>`
The simulation protocol.
gpu_support : bool
Whether to use package must have GPU support.
Returns
-------
(package, exe) : (str, str)
The name of the MD package and a path to its executable.
"""
# The input has already been validated in the run method, so no need
# to re-validate here.
# Get the file format of the molecular system.
fileformat = system.fileFormat()
# Make sure that this format is supported.
if not fileformat in _file_extensions:
raise ValueError("Cannot find an MD package that supports format: %s" %
fileformat)
else:
packages = _file_extensions[fileformat]
# Is this a free energy protocol.
if type(protocol) is _Protocol.FreeEnergy:
is_free_energy = True
else:
is_free_energy = False
# Loop over each package that supports the file format.
for package in packages:
# If this is free energy protocol, then check that the package has support.
if not is_free_energy or _free_energy[package]:
# Check whether this package exists on the system and has the desired
# GPU support.
for exe, gpu in _md_packages[package].items():
# If the user has requested GPU support make sure the package
# supports it.
if not gpu_support or gpu:
# AMBER
if package == "AMBER":
# Search AMBERHOME, if set.
if _amber_home is not None:
_exe = "%s/bin/%s" % (_amber_home, exe)
if _os.path.isfile(_exe):
return (package, _exe)
# Search system PATH.
else:
try:
exe = _SireBase.findExe(exe).absoluteFilePath()
return (package, exe)
except:
pass
# GROMACS
elif package == "GROMACS":
if _gmx_exe is not None:
return (package, _gmx_exe)
# SOMD
elif package == "SOMD":
return (package, _SireBase.getBinDir() + "/somd")
# Search system PATH.
else:
try:
exe = _SireBase.findExe(exe).absoluteFilePath()
return (package, exe)
except:
pass
# If we get this far, then no package was found.
raise _MissingSoftwareError("Couldn't find package to support format: %s" %
fileformat)