From 6a75d39825a6b713c0cd522318c33d88e9829772 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 2 Sep 2018 15:16:06 +0100 Subject: [PATCH 01/38] Adds basic framework for reading NCRST files --- package/MDAnalysis/coordinates/INPCRD.py | 124 +++++++++++++++++++++ package/MDAnalysis/coordinates/__init__.py | 3 + 2 files changed, 127 insertions(+) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 91a6c948b4f..2b54d713263 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -41,6 +41,21 @@ from six.moves import range from . import base +from ..core import flags +import scipy.io.netcdf +import warnings +import logging +import errno +import numpy as np + +logger = logging.getLogger("MDAnalysis.coordinates.AMBER") + +try: + import netCDF4 +except ImportError: + netCDF4 = None + logger.warning("netCDF4 is not available. Writing AMBER NCRST will be slow.") + class INPReader(base.SingleFrameReaderBase): """Reader for Amber restart files.""" @@ -82,3 +97,112 @@ def parse_n_atoms(filename, **kwargs): f.readline() n_atoms = int(f.readline().split()[0]) return n_atoms + + +class NCRSTReader(base.SingleFrameReaderBase): + """Reader for Amber NetCDF restart files. + To do: detailed information here. + """ + + format = ['NCRST', 'NCRESTRT'] + version = "1.0" + units = {'time': 'ps', + 'length': 'Angstrom', + 'velocity': 'Angstrom/ps', + 'forces': 'kcal/(mol*Angstrom)'} + + + def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs): + # Add optional mmap here + self._mmap = mmap + super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, **kwargs) + + + @staticmethod + def parse_natoms(filename, **kwargs): + with scipy.io.netcdf.netcdf_file(filename, mmap=None) as f: + n_atoms = f.dimensions['atom'] + return n_atoms + + + def _read_first_frame(self): + # Open netcdf file as a context manager + with scipy.io.netcdf.netcdf_file(self.filename, mmap=self._mmap) as rstfile: + # Check file contents + if not ('AMBERRESTART' in + rstfile.Conventions.decode('utf-8').split(',') or + 'AMBERRESTART' in + rstfile.Conventions.decode('utf-8').split()): + errmsg = ("NCDF restart file {0} does not conform to AMBER " + "specifications, http://ambermd.org/netcdf/nctraj.xhtml " + "('AMBERRESTART' must be one of the tokens in attribute " + "Conventions)".format(self.filename)) + logger.fatal(errmsg) + raise TypeError(errmsg) + + if not rstfile.ConventionVersion.decode('utf-8') == self.version: + wmsg = ("NCDF trajectory format is {0!s} but the reader " + "implements format {1!s}".format( + rstfile.ConventionVersion, self.version)) + warnings.warn(wmsg) + logger.warning(wmsg) + + if rstfile.variables['time'].units.decode('utf-8') != "picosecond": + raise NotImplementedError( + "NCRSTReader currently assumes that the trajectory was written " + "with a time unit of picoseconds and not {0}.".format( + rstfile.variables['time'].units)) + if rstfile.variables['coordinates'].units.decode('utf-8') != "angstrom": + raise NotImplementedError( + "NCRSTReader currently assumes that the trajectory was written " + "with a length unit of Angstroem and not {0}.".format( + rstfile.variables['coordinates'].units)) + if hasattr(rstfile.variables['coordinates'], 'scale_factor'): + raise NotImplementedError("scale_factors are not implemented") + + # Get remarks + try: + self.remarks = rstfile.title + except AttributeError: + self.remarks = "" + # Get n_atoms - Base class assigns self.n_atom to the passed value + # of n_atoms which make for a slightly confusing check + self.n_atoms = rstfile.dimensions['atom'] + if self.n_atom is not None and self.n_atom != self.n_atoms: + raise ValueError("Supplied n_atoms ({0}) != natom from ncdf ({1}). " + "Note: n_atoms can be None and then the ncdf value " + "is used!".format(n_atoms, self.n_atoms)) + + # Check for the presence of optional variables + self.has_velocities = 'velocities' in rstfile.variables + self.has_forces = 'forces' in rstfile.variables + self.periodic = 'cell_lengths' in rstfile.variables + # Set timestep + self.ts = self._Timestep(self.n_atom, + velocities=self.has_velocities, + forces=self.has_forces, + reader=self, + **self._ts_kwargs) + + # Fetch file data + self.ts._pos[:] = rstfile.variables['coordinates'][:] + self.ts.time = rstfile.variables['time'].getValue() + if self.has_velocities: + self.ts._velocities[:] = rstfile.variables['velocities'][:] + if self.has_forces: + self.ts._forces[:] = rstfile.variables['forces'][:] + if self.periodic: + self.ts._unitcell[:3] = rstfile.variables['cell_lengths'][:] + self.ts._unitcell[3:] = rstfile.variables['cell_angles'][:] + + # Convert units + if self.convert_units: + self.convert_pos_from_native(self.ts._pos) + self.convert_time_from_native(self.ts.time) + if self.has_velocities: + self.convert_velocities_from_native(self.ts._velocities, + inplace=True) + if self.has_forces: + self.convert_forces_from_native(self.ts._forces, inplace=True) + if self.periodic: + self.convert_pos_from_native(self.ts._unitcell[:3]) diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index 2706f492151..8000b8758d2 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -206,6 +206,9 @@ class can choose an appropriate reader automatically. | | | | optional `netcdf4-python`_ module (coordinates and | | | | | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`| +---------------+-----------+-------+------------------------------------------------------+ + | AMBER | ncrst, | r | binary (NetCDF) restart file | + | | ncrestrt | | Module :mod:`MDAnalysis.coordinates.INPCRD | + +---------------+-----------+-------+------------------------------------------------------+ | Brookhaven | pdb/ent | r/w | a relaxed PDB format (as used in MD simulations) | | [#a]_ | | | is read by default; Multiple frames (MODEL) | | | | | are supported but require the *multiframe* keyword. | From 5a881009a68e5de8b8561cc9836d6398fae21dbd Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 2 Sep 2018 18:53:56 +0100 Subject: [PATCH 02/38] Removing unused imports --- package/MDAnalysis/coordinates/INPCRD.py | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 2b54d713263..02b437fd567 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -41,21 +41,12 @@ from six.moves import range from . import base -from ..core import flags import scipy.io.netcdf import warnings import logging -import errno -import numpy as np logger = logging.getLogger("MDAnalysis.coordinates.AMBER") -try: - import netCDF4 -except ImportError: - netCDF4 = None - logger.warning("netCDF4 is not available. Writing AMBER NCRST will be slow.") - class INPReader(base.SingleFrameReaderBase): """Reader for Amber restart files.""" @@ -133,7 +124,7 @@ def _read_first_frame(self): rstfile.Conventions.decode('utf-8').split(',') or 'AMBERRESTART' in rstfile.Conventions.decode('utf-8').split()): - errmsg = ("NCDF restart file {0} does not conform to AMBER " + errmsg = ("NetCDF restart file {0} does not conform to AMBER " "specifications, http://ambermd.org/netcdf/nctraj.xhtml " "('AMBERRESTART' must be one of the tokens in attribute " "Conventions)".format(self.filename)) From 8b7dbd5c8100ae7d30f893d16153eb50f488a3f2 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 4 Sep 2018 14:23:35 +0100 Subject: [PATCH 03/38] Major updates to NCRST reader --- package/MDAnalysis/coordinates/INPCRD.py | 267 ++++++++++++++++++----- 1 file changed, 214 insertions(+), 53 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 02b437fd567..ae32aee32fa 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -21,20 +21,77 @@ # -"""INPCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD` +"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD` ================================================================================ -Read coordinates in Amber_ coordinate/restart file (suffix "inpcrd"). +AMBER_ can write :ref:`ASCII restart` ("inpcrd") and +:ref:`binary restart` ("ncrst") coordinate files. MDAnalysis +supports reading of both file formats. -.. _Amber: http://ambermd.org/formats.html#restart +.. rubric:: Units +AMBER restart files are assumed to be in the following units: -Classes -------- +* length in Angstrom (Å) +* time in ps +* velocity (NCRST only) in Å / ps +* force (NCRST only) in kcal / (mol * Å) + + +.. _ascii-restart: + +ASCII INPCRD restart files +-------------------------- + +ASCII AMBER_ INPCRD coordinate files (as defined in `AMBER INPCRD FORMAT`_) +are handled by the :class:`INPReader`. + +AMBER ASICC restart files are recognised by the suffix '.inpcrd', '.restrt', or +'.rst7' + +.. rubric:: Limitations + +* Box information is not read (or checked for). + +* Velocities are currently *not supported*. .. autoclass:: INPReader :members: + +.. _netcdf-restart: + +Binary NetCDF restart files +--------------------------- + +The `AMBER netcdf`_ restart format makes use of NetCDF_ (Network Common Data +Form) format. Such binary restart files are recognised in MDAnalysis by the +suffix '.ncrst' or '.ncrestrt' and read by the :class:`NCRSTReader`. + +Binary restart files can also contain velocity and force information, and can +record the simulation time step. Whilst the `AMBER netcdf`_ format details +default unit values of ångström and picoseconds, these can in theory occupy any +unit type. However, at the moment MDAnalysis only supports the default types +and will raise a :exc:`NotImplementedError` if anything else is detected. + +.. rubric:: Limitations + +* scale_factors are not supported (and not checked). +* Replica exchange variables are not supported. +* Restart files without coordinate information are not supported. + +.. autoclass:: NCRSTReader + :members: + + + +.. Links + +.. _AMBER: http://ambermd.org +.. _AMBER INPCRD FORMAT: http://ambermd.org/formats.html#restart +.. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml +.. _NetCDF: http://www.unidata.ucar.edu/software/netcdf + """ from __future__ import absolute_import, division, print_function, unicode_literals @@ -51,7 +108,7 @@ class INPReader(base.SingleFrameReaderBase): """Reader for Amber restart files.""" - format = ['INPCRD', 'RESTRT'] + format = ['INPCRD', 'RESTRT', 'RST7'] units = {'length': 'Angstrom'} def _read_first_frame(self): @@ -91,8 +148,52 @@ def parse_n_atoms(filename, **kwargs): class NCRSTReader(base.SingleFrameReaderBase): - """Reader for Amber NetCDF restart files. - To do: detailed information here. + """Reader for `AMBER NETCDF format`_ (version 1.0 rev C) restart files. + + This reader is :class:`SingleFrameReaderBase` adaptation of the + :class:`NCDFReader` AMBER NETCDF trajectory reader. + + AMBER binary restart files are automatically recognised by the file + extensions ".ncrst" and ".ncrestrt". + + The number of atoms (`n_atoms`) does not have to be provided as it can + be read from the input NETCDF file. + + Current simulation time is autodetected and read into the + :attr:`Timestep.time` attribute. (If this is not available in the restart + file, then :attr:`Timestep.time` will return 0.0 ps). + + Velocities are autodetected and read into the + :attr:`Timestep._velocities` attribute + + Forces are autodetected and read into the + :attr:`Timestep._forces` attribute + + Periodic unit cell information is detected and used to populate the + :attr:`Timestep.dimensions` attribute. (If not unit cell is available in + the restart file, then :attr:`Timestep.dimensions` will return + ``[0,0,0,0,0,0]``). + + Current limitations: + + * Only restart files with time in ps and lengths in Angstroem are processed + * scale_factors are not supported (and not checked) + * Restart files without coordinate information are not supported + * Replica exchange variables are not supported + + The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` + must be installed. It supports the *mmap* keyword argument as detailed in + :class:`NCDFReader`. + + .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml + + See Also + -------- + :class:`NCDFReader` + :class:`NCDFWriter` + + .. versionadded: 0.18.1 + """ format = ['NCRST', 'NCRESTRT'] @@ -102,12 +203,28 @@ class NCRSTReader(base.SingleFrameReaderBase): 'velocity': 'Angstrom/ps', 'forces': 'kcal/(mol*Angstrom)'} + class Timestep(base.Timestep): + """ Modified Timestep class for AMBER - def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs): - # Add optional mmap here - self._mmap = mmap - super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, **kwargs) + Uses C order memory mapping to match the style used AMBER TRAJ + + The Timestep can be initialized with `arg` being an integer + (the number of atoms) and an optional keyword arguments to allocate + space for velocities, and forces. + .. versionchanged:: 0.10.0 + Added ability to contain Forces + TODO: test if this actually impacts on performance / results + """ + order = 'C' + + _Timestep = Timestep + + def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, + **kwargs): + self._mmap = mmap + super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, + **kwargs) @staticmethod def parse_natoms(filename, **kwargs): @@ -115,85 +232,129 @@ def parse_natoms(filename, **kwargs): n_atoms = f.dimensions['atom'] return n_atoms - def _read_first_frame(self): - # Open netcdf file as a context manager + """Function to read NetCDF restart file and fill timestep + + Called by: :class:`SingleFrameReaderBase`.__init__ + Overrides :class:`SingleFrameReaderBase` placeholder function + """ with scipy.io.netcdf.netcdf_file(self.filename, mmap=self._mmap) as rstfile: - # Check file contents + # Global attribute checks + # Conventions should contain the AMBERRESTART string if not ('AMBERRESTART' in rstfile.Conventions.decode('utf-8').split(',') or 'AMBERRESTART' in rstfile.Conventions.decode('utf-8').split()): errmsg = ("NetCDF restart file {0} does not conform to AMBER " - "specifications, http://ambermd.org/netcdf/nctraj.xhtml " - "('AMBERRESTART' must be one of the tokens in attribute " - "Conventions)".format(self.filename)) + "specifications, as detailed in " + "http://ambermd.org/netcdf/nctraj.xhtml " + "('AMBERRESTART' must be one of the tokens in " + "attribute Conventions)".format(self.filename)) logger.fatal(errmsg) raise TypeError(errmsg) + # ConventionVersion should exist and be equal to 1.0 if not rstfile.ConventionVersion.decode('utf-8') == self.version: - wmsg = ("NCDF trajectory format is {0!s} but the reader " + wmsg = ("NCDF restart format is {0!s} but the reader " "implements format {1!s}".format( - rstfile.ConventionVersion, self.version)) + rstfile.ConventionVersion, self.version)) warnings.warn(wmsg) logger.warning(wmsg) - if rstfile.variables['time'].units.decode('utf-8') != "picosecond": - raise NotImplementedError( - "NCRSTReader currently assumes that the trajectory was written " - "with a time unit of picoseconds and not {0}.".format( - rstfile.variables['time'].units)) - if rstfile.variables['coordinates'].units.decode('utf-8') != "angstrom": - raise NotImplementedError( - "NCRSTReader currently assumes that the trajectory was written " - "with a length unit of Angstroem and not {0}.".format( - rstfile.variables['coordinates'].units)) + # The use of scale_factor is currently unsupported if hasattr(rstfile.variables['coordinates'], 'scale_factor'): raise NotImplementedError("scale_factors are not implemented") - # Get remarks - try: - self.remarks = rstfile.title - except AttributeError: - self.remarks = "" - # Get n_atoms - Base class assigns self.n_atom to the passed value - # of n_atoms which make for a slightly confusing check - self.n_atoms = rstfile.dimensions['atom'] - if self.n_atom is not None and self.n_atom != self.n_atoms: - raise ValueError("Supplied n_atoms ({0}) != natom from ncdf ({1}). " - "Note: n_atoms can be None and then the ncdf value " - "is used!".format(n_atoms, self.n_atoms)) - - # Check for the presence of optional variables + # Note: SingleFrameReaderBase class sets parsed n_atoms value to + # self.n_atom which makes for a confusing check + if 'atom' in rstfile.dimensions: + self.n_atoms = rstfile.dimensions['atom'] + if self.n_atom is not None and self.n_atom != self.n_atoms: + raise ValueError("Supplied n_atoms ({0}) != n_atoms from " + "NetCDF restart file ({1}). " + "Note: n_atoms can be None and then the " + "restart file value is used.".format( + self.n_atom, self.n_atoms)) + else: + errmsg = ("NetCDF restart file {0} does not contain " + "atom information ".format(self.filename)) + logger.fatal(errmsg) + raise TypeError(errmsg) + + # Optional variables self.has_velocities = 'velocities' in rstfile.variables self.has_forces = 'forces' in rstfile.variables self.periodic = 'cell_lengths' in rstfile.variables + # Set timestep - self.ts = self._Timestep(self.n_atom, + self.ts = self._Timestep(self.n_atoms, velocities=self.has_velocities, forces=self.has_forces, reader=self, **self._ts_kwargs) - # Fetch file data - self.ts._pos[:] = rstfile.variables['coordinates'][:] - self.ts.time = rstfile.variables['time'].getValue() + # NetCDF file title is optional + try: + self.remarks = rstfile.title + except AttributeError: + self.remarks = "" + + # Default to time units of picoseconds + # Note: unlike trajectories the AMBER NetCDF convention allows + # restart files to omit time when unecessary (i.e. minimizations) + if 'time' in rstfile.variables: + units = rstfile.variables['time'].units.decode('utf-8') + if units != "picosecond": + raise NotImplementedError( + "NCRSTReader currently assumes that the restart file " + "uses a time unit of picoseconds and not {0}.".format( + rstfile.variables['time'].units)) + self.ts.time = rstfile.variables['time'].getValue() + else: + # As of AMBER16 the NetCDF restart files created by + # minimizations ignore convention and default to 0.0, so we do + # the same here + self.ts.time = 0.0 + + # Default to length units of Angstroem + if 'coordinates' in rstfile.variables: + units = rstfile.variables['coordinates'].units.decode('utf-8') + if units != "angstrom": + raise NotImplementedError( + "NCRSTReader currently assumes that the restart file " + "uses a length unit of Angstroem and not {0}.".format( + rstfile.variables['coordinates'].units)) + self.ts._pos[:] = rstfile.variables['coordinates'][:] + else: + # Technically coordinate information is not required, however + # the lack of it in a restart file is highly unlikely + errmsg = ("NetCDF restart file {0} is missing coordinate " + "information ".format(self.filename)) + logger.fatal(errmsg) + raise TypeError(errmsg) + if self.has_velocities: self.ts._velocities[:] = rstfile.variables['velocities'][:] + + # The presence of forces in a restart file is very rare, but + # according to AMBER convention it can exist. if self.has_forces: self.ts._forces[:] = rstfile.variables['forces'][:] + + # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] if self.periodic: self.ts._unitcell[:3] = rstfile.variables['cell_lengths'][:] self.ts._unitcell[3:] = rstfile.variables['cell_angles'][:] - # Convert units + # Convert units inplace if self.convert_units: self.convert_pos_from_native(self.ts._pos) self.convert_time_from_native(self.ts.time) if self.has_velocities: self.convert_velocities_from_native(self.ts._velocities, inplace=True) - if self.has_forces: - self.convert_forces_from_native(self.ts._forces, inplace=True) - if self.periodic: - self.convert_pos_from_native(self.ts._unitcell[:3]) + if self.has_forces: + self.convert_forces_from_native(self.ts._forces, + inplace=True) + if self.periodic: + self.convert_pos_from_native(self.ts._unitcell[:3]) From 0c457ce65dd06b41b6d5df958ce785afedabb52d Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 5 Sep 2018 15:03:48 +0100 Subject: [PATCH 04/38] Try/except instead of it statements + docstring changes --- package/MDAnalysis/coordinates/INPCRD.py | 69 ++++++++++++------------ 1 file changed, 35 insertions(+), 34 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index ae32aee32fa..e8a2d7b589a 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -49,12 +49,6 @@ AMBER ASICC restart files are recognised by the suffix '.inpcrd', '.restrt', or '.rst7' -.. rubric:: Limitations - -* Box information is not read (or checked for). - -* Velocities are currently *not supported*. - .. autoclass:: INPReader :members: @@ -66,7 +60,7 @@ The `AMBER netcdf`_ restart format makes use of NetCDF_ (Network Common Data Form) format. Such binary restart files are recognised in MDAnalysis by the -suffix '.ncrst' or '.ncrestrt' and read by the :class:`NCRSTReader`. +suffix '.ncrst', '.ncrestrt' or '.ncrst7' and read by the :class:`NCRSTReader`. Binary restart files can also contain velocity and force information, and can record the simulation time step. Whilst the `AMBER netcdf`_ format details @@ -74,12 +68,6 @@ unit type. However, at the moment MDAnalysis only supports the default types and will raise a :exc:`NotImplementedError` if anything else is detected. -.. rubric:: Limitations - -* scale_factors are not supported (and not checked). -* Replica exchange variables are not supported. -* Restart files without coordinate information are not supported. - .. autoclass:: NCRSTReader :members: @@ -106,7 +94,14 @@ class INPReader(base.SingleFrameReaderBase): - """Reader for Amber restart files.""" + """Reader for Amber restart files. + + .. rubric:: Limitations + + * Box information is not read (or checked for). + * Velocities are currently *not supported*. + + """ format = ['INPCRD', 'RESTRT', 'RST7'] units = {'length': 'Angstrom'} @@ -154,7 +149,7 @@ class NCRSTReader(base.SingleFrameReaderBase): :class:`NCDFReader` AMBER NETCDF trajectory reader. AMBER binary restart files are automatically recognised by the file - extensions ".ncrst" and ".ncrestrt". + extensions ".ncrst", ".ncrestrt", and ".ncrst7". The number of atoms (`n_atoms`) does not have to be provided as it can be read from the input NETCDF file. @@ -174,17 +169,20 @@ class NCRSTReader(base.SingleFrameReaderBase): the restart file, then :attr:`Timestep.dimensions` will return ``[0,0,0,0,0,0]``). - Current limitations: + The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` + must be installed. It supports the *mmap* keyword argument as detailed in + :class:`NCDFReader`. + + The NCRST reader also uses a custom Timestep object with C-style memory + mapping in order to match the NCDFReader. + + .. rubric:: Limitations * Only restart files with time in ps and lengths in Angstroem are processed * scale_factors are not supported (and not checked) * Restart files without coordinate information are not supported * Replica exchange variables are not supported - The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` - must be installed. It supports the *mmap* keyword argument as detailed in - :class:`NCDFReader`. - .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml See Also @@ -196,7 +194,7 @@ class NCRSTReader(base.SingleFrameReaderBase): """ - format = ['NCRST', 'NCRESTRT'] + format = ['NCRST', 'NCRESTRT', 'NCRST7'] version = "1.0" units = {'time': 'ps', 'length': 'Angstrom', @@ -214,7 +212,6 @@ class Timestep(base.Timestep): .. versionchanged:: 0.10.0 Added ability to contain Forces - TODO: test if this actually impacts on performance / results """ order = 'C' @@ -227,7 +224,7 @@ def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs) @staticmethod - def parse_natoms(filename, **kwargs): + def parse_n_atoms(filename, **kwargs): with scipy.io.netcdf.netcdf_file(filename, mmap=None) as f: n_atoms = f.dimensions['atom'] return n_atoms @@ -267,7 +264,7 @@ def _read_first_frame(self): # Note: SingleFrameReaderBase class sets parsed n_atoms value to # self.n_atom which makes for a confusing check - if 'atom' in rstfile.dimensions: + try: self.n_atoms = rstfile.dimensions['atom'] if self.n_atom is not None and self.n_atom != self.n_atoms: raise ValueError("Supplied n_atoms ({0}) != n_atoms from " @@ -275,11 +272,11 @@ def _read_first_frame(self): "Note: n_atoms can be None and then the " "restart file value is used.".format( self.n_atom, self.n_atoms)) - else: + except KeyError: errmsg = ("NetCDF restart file {0} does not contain " "atom information ".format(self.filename)) logger.fatal(errmsg) - raise TypeError(errmsg) + raise KeyError(errmsg) # Optional variables self.has_velocities = 'velocities' in rstfile.variables @@ -302,7 +299,7 @@ def _read_first_frame(self): # Default to time units of picoseconds # Note: unlike trajectories the AMBER NetCDF convention allows # restart files to omit time when unecessary (i.e. minimizations) - if 'time' in rstfile.variables: + try: units = rstfile.variables['time'].units.decode('utf-8') if units != "picosecond": raise NotImplementedError( @@ -310,14 +307,18 @@ def _read_first_frame(self): "uses a time unit of picoseconds and not {0}.".format( rstfile.variables['time'].units)) self.ts.time = rstfile.variables['time'].getValue() - else: + except KeyError: # As of AMBER16 the NetCDF restart files created by - # minimizations ignore convention and default to 0.0, so we do - # the same here + # minimizations ignore convention and default to 0.0 ps + # Warn and do the same thing here + wmsg = ("Restart file {0} does not contain time information " + "time will default to 0.0 ps").format(self.filename) + warnings.warn(wmsg) + logger.warning(wmsg) self.ts.time = 0.0 # Default to length units of Angstroem - if 'coordinates' in rstfile.variables: + try: units = rstfile.variables['coordinates'].units.decode('utf-8') if units != "angstrom": raise NotImplementedError( @@ -325,19 +326,19 @@ def _read_first_frame(self): "uses a length unit of Angstroem and not {0}.".format( rstfile.variables['coordinates'].units)) self.ts._pos[:] = rstfile.variables['coordinates'][:] - else: + except KeyError: # Technically coordinate information is not required, however # the lack of it in a restart file is highly unlikely errmsg = ("NetCDF restart file {0} is missing coordinate " "information ".format(self.filename)) logger.fatal(errmsg) - raise TypeError(errmsg) + raise KeyError(errmsg) if self.has_velocities: self.ts._velocities[:] = rstfile.variables['velocities'][:] # The presence of forces in a restart file is very rare, but - # according to AMBER convention it can exist. + # according to AMBER convention, it can exist. if self.has_forces: self.ts._forces[:] = rstfile.variables['forces'][:] From d245e33335ca3cf87e2ccadac6e9e153bd6483d7 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Fri, 7 Sep 2018 18:22:26 +0100 Subject: [PATCH 05/38] 64 bit offset check --- package/MDAnalysis/coordinates/INPCRD.py | 37 +++++++++++++++++------- 1 file changed, 26 insertions(+), 11 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index e8a2d7b589a..fdb781b4aa4 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -158,11 +158,11 @@ class NCRSTReader(base.SingleFrameReaderBase): :attr:`Timestep.time` attribute. (If this is not available in the restart file, then :attr:`Timestep.time` will return 0.0 ps). - Velocities are autodetected and read into the - :attr:`Timestep._velocities` attribute + Velocities are autodetected and read into the :attr:`Timestep._velocities` + attribute. - Forces are autodetected and read into the - :attr:`Timestep._forces` attribute + Forces are autodetected and read into the :attr:`Timestep._forces` + attribute. Periodic unit cell information is detected and used to populate the :attr:`Timestep.dimensions` attribute. (If not unit cell is available in @@ -170,18 +170,18 @@ class NCRSTReader(base.SingleFrameReaderBase): ``[0,0,0,0,0,0]``). The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` - must be installed. It supports the *mmap* keyword argument as detailed in - :class:`NCDFReader`. + must be installed. Support for the *mmap* keyword is available as detailed + in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. The NCRST reader also uses a custom Timestep object with C-style memory mapping in order to match the NCDFReader. .. rubric:: Limitations - * Only restart files with time in ps and lengths in Angstroem are processed - * scale_factors are not supported (and not checked) - * Restart files without coordinate information are not supported - * Replica exchange variables are not supported + * Only NCRST files with time in ps and lengths in Angstroem are processed. + * scale_factors are not supported (and not checked). + * Restart files without coordinate information are not supported. + * Replica exchange variables are not supported. .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml @@ -219,6 +219,7 @@ class Timestep(base.Timestep): def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs): + # Assign input mmap value self._mmap = mmap super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, **kwargs) @@ -235,7 +236,8 @@ def _read_first_frame(self): Called by: :class:`SingleFrameReaderBase`.__init__ Overrides :class:`SingleFrameReaderBase` placeholder function """ - with scipy.io.netcdf.netcdf_file(self.filename, mmap=self._mmap) as rstfile: + # Open netcdf file via context manager + with scipy.io.netcdf.netcdf_file(self.filename, mode='r', mmap=self._mmap) as rstfile: # Global attribute checks # Conventions should contain the AMBERRESTART string if not ('AMBERRESTART' in @@ -250,6 +252,16 @@ def _read_first_frame(self): logger.fatal(errmsg) raise TypeError(errmsg) + # The AMBER NetCDF standard enforces 64 bit offsets + if not rstfile.version_byte == 2: + errmsg = ("NetCDF restart file {0} does not conform to AMBER " + "specifications, as details in " + "http://ambermd.org/netcdf/nctraj.xhtml " + "(NetCDF file does not use 64 bit offsets " + "[version_byte = 2]) ".format(self.filename)) + logger.fatal(errmsg) + raise TypeError(errmsg) + # ConventionVersion should exist and be equal to 1.0 if not rstfile.ConventionVersion.decode('utf-8') == self.version: wmsg = ("NCDF restart format is {0!s} but the reader " @@ -317,6 +329,9 @@ def _read_first_frame(self): logger.warning(wmsg) self.ts.time = 0.0 + # Single frame so we assign it to 0 + self.ts.frame = 0 + # Default to length units of Angstroem try: units = rstfile.variables['coordinates'].units.decode('utf-8') From b42003241098e443dd0cbf34ee73500c60d7b0f9 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 28 May 2019 11:18:01 +0100 Subject: [PATCH 06/38] Need to check things --- package/MDAnalysis/coordinates/INPCRD.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 7c6594fb5db..c6a041b02d3 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -146,7 +146,7 @@ def parse_n_atoms(filename, **kwargs): class NCRSTReader(base.SingleFrameReaderBase): """Reader for `AMBER NETCDF format`_ (version 1.0 rev C) restart files. - This reader is :class:`SingleFrameReaderBase` adaptation of the + This reader is a :class:`SingleFrameReaderBase` adaptation of the :class:`NCDFReader` AMBER NETCDF trajectory reader. AMBER binary restart files are automatically recognised by the file @@ -323,7 +323,7 @@ def _read_first_frame(self): except KeyError: # As of AMBER16 the NetCDF restart files created by # minimizations ignore convention and default to 0.0 ps - # Warn and do the same thing here + # Warn and do the same thing here (IA: need to check this) wmsg = ("Restart file {0} does not contain time information " "time will default to 0.0 ps").format(self.filename) warnings.warn(wmsg) From 767674147c3937d396a426ed7f9152b76b4a63a2 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 5 Aug 2019 10:49:48 +0100 Subject: [PATCH 07/38] Some changes --- package/MDAnalysis/coordinates/INPCRD.py | 40 ++++++++++++------------ 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index c6a041b02d3..add21c30727 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -65,15 +65,14 @@ Binary restart files can also contain velocity and force information, and can record the simulation time step. Whilst the `AMBER netcdf`_ format details -default unit values of ångström and picoseconds, these can in theory occupy any -unit type. However, at the moment MDAnalysis only supports the default types -and will raise a :exc:`NotImplementedError` if anything else is detected. +default unit values of ångström and picoseconds, these can in theory occupy +any unit type. However, at the moment MDAnalysis only supports the default +types and will raise a :exc:`NotImplementedError` if anything else is detected. .. autoclass:: NCRSTReader :members: - .. Links .. _AMBER: http://ambermd.org @@ -166,13 +165,18 @@ class NCRSTReader(base.SingleFrameReaderBase): attribute. Periodic unit cell information is detected and used to populate the - :attr:`Timestep.dimensions` attribute. (If not unit cell is available in + :attr:`Timestep.dimensions` attribute. (If no unit cell is available in the restart file, then :attr:`Timestep.dimensions` will return ``[0,0,0,0,0,0]``). The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` - must be installed. Support for the *mmap* keyword is available as detailed - in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. + must be installed. + + Support for the *mmap* keyword is available as detailed + in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. When + mmap = True, the +It is + enabled by default The NCRST reader also uses a custom Timestep object with C-style memory mapping in order to match the NCDFReader. @@ -180,7 +184,7 @@ class NCRSTReader(base.SingleFrameReaderBase): .. rubric:: Limitations * Only NCRST files with time in ps and lengths in Angstroem are processed. - * scale_factors are not supported (and not checked). + * scale_factors are not supported (raises NotImplementedError). * Restart files without coordinate information are not supported. * Replica exchange variables are not supported. @@ -191,7 +195,7 @@ class NCRSTReader(base.SingleFrameReaderBase): :class:`NCDFReader` :class:`NCDFWriter` - .. versionadded: 0.18.1 + .. versionadded: 0.20.0 """ @@ -205,14 +209,11 @@ class NCRSTReader(base.SingleFrameReaderBase): class Timestep(base.Timestep): """ Modified Timestep class for AMBER - Uses C order memory mapping to match the style used AMBER TRAJ + Uses C order memory mapping to match the style used by AMBER TRAJ The Timestep can be initialized with `arg` being an integer (the number of atoms) and an optional keyword arguments to allocate space for velocities, and forces. - - .. versionchanged:: 0.10.0 - Added ability to contain Forces """ order = 'C' @@ -321,14 +322,13 @@ def _read_first_frame(self): rstfile.variables['time'].units)) self.ts.time = rstfile.variables['time'].getValue() except KeyError: - # As of AMBER16 the NetCDF restart files created by - # minimizations ignore convention and default to 0.0 ps - # Warn and do the same thing here (IA: need to check this) - wmsg = ("Restart file {0} does not contain time information " - "time will default to 0.0 ps").format(self.filename) + # Warn the user and move on + wmsg = ("Restart file {0} does not contain time information. " + "This is should be expected if the file was not " + "created from an MD trajectory (e.g. a " + "minimization)".format(self.filename)) warnings.warn(wmsg) logger.warning(wmsg) - self.ts.time = 0.0 # Single frame so we assign it to 0 self.ts.frame = 0 @@ -338,7 +338,7 @@ def _read_first_frame(self): units = rstfile.variables['coordinates'].units.decode('utf-8') if units != "angstrom": raise NotImplementedError( - "NCRSTReader currently assumes that the restart file " + "NCRSTReader currently expects that the restart file " "uses a length unit of Angstroem and not {0}.".format( rstfile.variables['coordinates'].units)) self.ts._pos[:] = rstfile.variables['coordinates'][:] From df2416821abf6b7bf8b14f7b4df5f5627df37848 Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 6 Aug 2019 09:19:30 +0100 Subject: [PATCH 08/38] Exception + Minor docs update --- package/MDAnalysis/coordinates/INPCRD.py | 37 +++++++++++++++++----- package/MDAnalysis/coordinates/__init__.py | 6 ++-- 2 files changed, 33 insertions(+), 10 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index add21c30727..7aed8474d26 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -170,13 +170,14 @@ class NCRSTReader(base.SingleFrameReaderBase): ``[0,0,0,0,0,0]``). The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` - must be installed. + must be installed. Support for the *mmap* keyword is available as detailed - in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. When - mmap = True, the -It is - enabled by default + in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. The use of + ``mmap=True`` leads to around a 2x read speed improvement in a ~ 1 million + atom system (AMBER STMV benchmark). As per the :class:`NCDFReader`, the + default behaviour is ``mmap=None``, which means that the default behaviour + of :class:`scipy.io.netcdf.netcdf_file` prevails. The NCRST reader also uses a custom Timestep object with C-style memory mapping in order to match the NCDFReader. @@ -239,7 +240,8 @@ def _read_first_frame(self): Overrides :class:`SingleFrameReaderBase` placeholder function """ # Open netcdf file via context manager - with scipy.io.netcdf.netcdf_file(self.filename, mode='r', mmap=self._mmap) as rstfile: + with scipy.io.netcdf.netcdf_file(self.filename, mode='r', + mmap=self._mmap) as rstfile: # Global attribute checks # Conventions should contain the AMBERRESTART string if not ('AMBERRESTART' in @@ -264,14 +266,33 @@ def _read_first_frame(self): logger.fatal(errmsg) raise TypeError(errmsg) + # The specs require that dimensions->spatial == 3 exists + try: + if not rstfile.dimensions['spatial'] == 3: + errmsg = "Incorrect spatial value for NCRST file" + raise TypeError(errmsg) + except KeyError: + errmsg = "NCRST file does not contain sptial dimension" + raise KeyError(errmsg) + # ConventionVersion should exist and be equal to 1.0 if not rstfile.ConventionVersion.decode('utf-8') == self.version: - wmsg = ("NCDF restart format is {0!s} but the reader " - "implements format {1!s}".format( + wmsg = ("NCRST format is {0!s} but the reader implements " + "format {1!s}".format( rstfile.ConventionVersion, self.version)) warnings.warn(wmsg) logger.warning(wmsg) + # The specs define Program and ProgramVersion as required. Here we + # just warn the users instead of raising an Error. + if not (hasattr(rstfile, 'program') or + hasattr(rstfile, 'programVersion')): + wmsg = ("This NCRST file may not fully adhere to AMBER " + "standards as either the `program` or " + "`programVersion` attributes are missing") + warnings.warn(wmsg) + logger.warning(wmsg) + # The use of scale_factor is currently unsupported if hasattr(rstfile.variables['coordinates'], 'scale_factor'): raise NotImplementedError("scale_factors are not implemented") diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index abd37fd0b90..6d9dc35be18 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -201,14 +201,16 @@ class can choose an appropriate reader automatically. | | | | Module :mod:`MDAnalysis.coordinates.TRJ` | +---------------+-----------+-------+------------------------------------------------------+ | AMBER | inpcrd, | r | formatted (ASCII) coordinate/restart file | - | | restrt | | Module :mod:`MDAnalysis.coordinates.INPCRD` | + | | restrt, | | Module :mod:`MDAnalysis.coordinates.INPCRD` | + | | rst7 | | | +---------------+-----------+-------+------------------------------------------------------+ | AMBER | ncdf, nc | r/w | binary (NetCDF) trajectories are fully supported with| | | | | optional `netcdf4-python`_ module (coordinates and | | | | | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`| +---------------+-----------+-------+------------------------------------------------------+ | AMBER | ncrst, | r | binary (NetCDF) restart file | - | | ncrestrt | | Module :mod:`MDAnalysis.coordinates.INPCRD | + | | ncrestrt, | | Module :mod:`MDAnalysis.coordinates.INPCRD | + | | ncrst7 | | | +---------------+-----------+-------+------------------------------------------------------+ | Brookhaven | pdb/ent | r/w | a relaxed PDB format (as used in MD simulations) | | [#a]_ | | | is read by default; Multiple frames (MODEL) | From 93f2edb5e7547c0cbb63caa44e1034c374fc6759 Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 6 Aug 2019 21:34:49 +0100 Subject: [PATCH 09/38] More exceptions + start on tests --- package/MDAnalysis/coordinates/INPCRD.py | 52 +-- .../MDAnalysisTests/coordinates/test_ncrst.py | 299 ++++++++++++++++++ 2 files changed, 331 insertions(+), 20 deletions(-) create mode 100644 testsuite/MDAnalysisTests/coordinates/test_ncrst.py diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 7aed8474d26..f76b95bb490 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -244,17 +244,21 @@ def _read_first_frame(self): mmap=self._mmap) as rstfile: # Global attribute checks # Conventions should contain the AMBERRESTART string - if not ('AMBERRESTART' in - rstfile.Conventions.decode('utf-8').split(',') or - 'AMBERRESTART' in - rstfile.Conventions.decode('utf-8').split()): - errmsg = ("NetCDF restart file {0} does not conform to AMBER " - "specifications, as detailed in " - "http://ambermd.org/netcdf/nctraj.xhtml " - "('AMBERRESTART' must be one of the tokens in " - "attribute Conventions)".format(self.filename)) - logger.fatal(errmsg) - raise TypeError(errmsg) + try: + if not ('AMBERRESTART' in + rstfile.Conventions.decode('utf-8').split(',') or + 'AMBERRESTART' in + rstfile.Conventions.decode('utf-8').split()): + errmsg = ("NetCDF restart file {0} does not conform to " + "AMBER specifications, as detailed in " + "http://ambermd.org/netcdf/nctraj.xhtml " + "('AMBERRESTART' must be one of the tokens in " + "attribute Conventions)".format(self.filename)) + logger.fatal(errmsg) + raise TypeError(errmsg) + except KeyError: + errmsg = "NetCDF file is missign Conventions" + raise KeyError(errmsg) # The AMBER NetCDF standard enforces 64 bit offsets if not rstfile.version_byte == 2: @@ -275,13 +279,18 @@ def _read_first_frame(self): errmsg = "NCRST file does not contain sptial dimension" raise KeyError(errmsg) - # ConventionVersion should exist and be equal to 1.0 - if not rstfile.ConventionVersion.decode('utf-8') == self.version: - wmsg = ("NCRST format is {0!s} but the reader implements " - "format {1!s}".format( - rstfile.ConventionVersion, self.version)) - warnings.warn(wmsg) - logger.warning(wmsg) + try: + # ConventionVersion should exist and be equal to 1.0 + if not rstfile.ConventionVersion.decode('utf-8') == + self.version: + wmsg = ("NCRST format is {0!s} but the reader implements " + "format {1!s}".format( + rstfile.ConventionVersion, self.version)) + warnings.warn(wmsg) + logger.warning(wmsg) + except KeyError: + errmsg = "ConventionVersion not present in NetCDF file" + raise KeyError(errmsg) # The specs define Program and ProgramVersion as required. Here we # just warn the users instead of raising an Error. @@ -294,8 +303,11 @@ def _read_first_frame(self): logger.warning(wmsg) # The use of scale_factor is currently unsupported - if hasattr(rstfile.variables['coordinates'], 'scale_factor'): - raise NotImplementedError("scale_factors are not implemented") + # Note scale_factor can be an attribute of any variable + for variable in rstfile.variables: + if hasattr(rstfile.variables[variable], 'scale_factor'): + errmsg = "scale_factors are not implemented" + raise NotImplementedError(errmsg) # Note: SingleFrameReaderBase class sets parsed n_atoms value to # self.n_atom which makes for a confusing check diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py new file mode 100644 index 00000000000..de3e0583f89 --- /dev/null +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -0,0 +1,299 @@ +# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- +# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 +# +# MDAnalysis --- https://www.mdanalysis.org +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# +# Released under the GNU Public Licence, v2 or any higher version +# +# Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# doi: 10.25080/majora-629e541a-00e +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# +from __future__ import absolute_import +import MDAnalysis as mda +import numpy as np +from scipy.io import netcdf +from MDAnalysis.coordinates.INPCRD import NCRSTReader +import pytest +from numpy.testing import ( + assert_equal, + assert_almost_equal +) + +from MDAnalysisTests.datafiles import (PFncdf_Top, PFncdf_Trj, + GRO, TRR, XYZ_mini) +from MDAnalysisTests.coordinates.reference import (RefVGV, RefTZ2) + + +class _NCRestartTest(object): + + prec = 5 + + @pytest.fixture(scope='class') + def universe(self): + return mda.Universe(self.topology, self.filename, mmap=self.mmap) + + def test_wrong_natoms(self): + with pytest.raises(ValueError): + NCRSTReader(self.filename, n_atoms=2, mmap=self.mmap) + + def test_mmap_value(self): + reader = NCRSTReader(self.filename, mmap=self.mmap) + if not self.mmap: + assert_equal(reader._mmap, None) + else: + assert_equal(reader._mmap, self.mmap) + + def test_remarks(self, universe): + title = universe.trajectory.remarks.decode('utf-8') + assert_equal(self.title, title) + + def test_n_atoms(self, universe): + assert_equal(self.n_atoms, len(universe.atoms)) + + def test_numres(self, universe): + assert_equal(self.n_res, len(universe.residues)) + + def test_time(self, universe): + assert_equal(self.time, universe.trajectory.time) + + def test_frame(self, universe): + assert_equal(universe.trajectory.frame, 0) + + # Test slices as per base + def test_full_slice(self, universe): + trj_iter = universe.trajectory[:] + frames = [ts.frame for ts in trj_iter] + assert_equal(frames, np.arange(universe.trajectory.n_frames)) + + def test_last_slice(self, universe): + trj_iter = universe.trajectory[-1:] + frames = [ts.frame for ts in trj_iter] + assert_equal(frames, np.arange(universe.trajectory.n_frames)) + + def test_num_frames(self, universe): + assert_equal(universe.trajectory.n_frames, 1) + + def test_dt(self, universe): + with pytest.warns(UserWarning) as record: + assert_equal(universe.trajectory.dt, 1.0) + + assert len(record) == 1 + wmsg = "Reader has no dt information, set to 1.0 ps" + assert str(record[0].message.args[0]) == wmsg + + def test_units(self, universe): + units = {'time': 'ps', 'length': 'Angstrom', + 'velocity': 'Angstrom/ps', 'force': 'kcal/(mol*Angstrom)'} + assert_equal(universe.trajectory.units, units) + + def test_has_velocities(self, universe): + assert_equal(self.has_velocities, universe.trajectory.has_velocities) + + def test_has_forces(self, universe): + assert_equal(self.has_forces, universe.trajectory.has_forces) + + +class Read_ACECFV(_NCRestartTest): + """ACE in water with Coordinates, Forces and Velocities""" + + # Placeholder values + # topology = ACE + # filename = ACE-PARM7 + title = 'Cpptraj Generated Restart' + n_atoms = 1398 + n_res = 465 + time = 1.0 + has_velocities = True + has_forces = True + + def test_positions(self, universe, selstr, expected): + ag = universe.select_atoms(selstr) + assert_almost_equal(expected, ag.positions, self.prec) + + def test_velocities(self, universe, selstr, expected): + ag = universe.select_atoms(selstr) + assert_almost_equal(expected, ag.velocities, self.prec) + + def test_forces(self, universe, selstr, expected): + ag = universe.select_atoms(selstr) + # We convert from kj back to the original kcal value + assert_almost_equal(expected, ag.forces * 4.184, self.prec) + + +class ExceptionsNCRSTGenerator(object): + """A basic modular ncrst writer based on :class:`NCDFWriter`""" + + def create_ncrst(self): + # Create under context manager + with netcdf.netcdf_file(self.filename, mode='w', + version=self.version_byte) as ncrst: + # Top level attributes + if self.Conventions: + setattr(ncrst, 'Conventions', self.Conventions) + if self.ConventionVersion: + setattr(ncrst, 'ConventionVersion', self.ConventionVersion) + if self.program: + setattr(ncrst, 'program', self.program) + if self.programVersion: + setattr(ncrst, 'programVersion', self.programVersion) + + # Dimensions + if self.n_atoms: + ncrst.createDimension('atom', self.n_atoms) + if self.spatial: + ncrst.createDimension('spatial', self.spatial) + + # Variables + if self.time: + time = ncrst.createVariable('time', 'f8') + time = 1.0 + setattr(time, 'units', self.time) + # Spatial or atom dependent variables + if (self.spatial) and (self.n_atoms): + if self.coords: + coords = ncrst.createVariable('coordinates', 'f8', + ('atom', 'spatial')) + setattr(coords, 'units', self.coords) + coords[:] = np.asarray(range(self.spatial), + dtype=np.float32) + spatial = ncrst.createVariable('spatial', 'c', ('spatial',)) + spatial[:] = np.asarray(list('xyz')) + velocs = ncrst.createVariable('velocities', 'f8', + ('atom', 'spatial')) + setattr(velocs, 'units', 'angstrom/picosecond') + velocs[:] = np.asarray(range(self.spatial), dtype=np.float32) + forces = ncrst.createVariable('forces', 'f8', + ('atom', 'spatial')) + setattr(forces, 'units', 'kilocalorie/mole/angstrom') + forces[:] = np.asarray(range(self.spatial), dtype=np.float32) + + # self.scale_factor overrides which variable gets a scale_factor + if self.scale_factor: + setattr(ncrst.variables[self.scale_factor], + 'scale_factor', 2.0) + + # Default definitions + filename = 'test.ncrst' + version_byte = 2 + Conventions = 'AMBERRESTART' + ConventionVersion = '1.0' + program = 'mda test_writer' + programVersion = 'V42' + n_atoms = 1 + spatial = 3 + coords = 'angstrom' + time = 'picosecond' + scale_factor = None + + +def TestNCRSTReaderExceptions(ExceptionsNCRSTGenerator): + + # TO DO: merge these so you get TypeErrors, KeyErrors, etc... + + def test_VersionbyteError(self, tmpdir): + self.version_byte = 1 + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(TypeError): + NCRSTReader(self.filename) + + def test_WrongConventionsError(self, tmpdir): + self.Conventions = 'Foo' + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(TypeError): + NCRSTReader(self.filename) + + def test_NoConventionsError(self, tmpdir): + self.Conventions = None + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(KeyError): + NCRSTReader(self.filename) + + def test_WrongConventionVersionError(self, tmpdir): + self.ConventionVersion = '2.0' + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(TypeError): + NCRSTReader(self.filename) + + def test_NoConventionVersionError(self, tmpdir): + self.ConventionVersion = None + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(KeyError): + NCRSTReader(self.filename) + + def test_WrongSpatialError(self, tmpdir): + self.spatial = 2 + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(TypeError): + NCRSTReader(self.filename) + + def test_NoSpatialError(self, tmpdir): + self.spatial = None + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(KeyError): + NCRSTReader(self.filename) + + def test_NoAtomsError(self, tmpdir): + self.n_atoms = None + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(KeyError): + NCRSTReader(self.filename) + + def test_WrongTimeError(self, tmpdir): + self.time = 'femtosecond' + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(NotImplementedError): + NCRSTReader(self.filename) + + def test_WrongCoordsError(self, tmpdir): + self.coords = 'nanometer' + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(NotImplementedError): + NCRSTReader(self.filename) + + def test_NoCoordsError(self, tmpdir): + self.coords = None + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(KeyError): + NCRSTReader(self.filename) + + @pytest.mark.parametrize('variable', [ + 'time', 'coordinates', 'spatial', + 'velocities', 'forces' + ]) + def test_scale_factor(self, tmpdir, variable): + self.scale_factor = variable + with tmpdir.as_cwd(): + self.create_ncrst() + with pytest.raises(NotImplementedError): + NCRSTReader(self.filename) + +# Errors: +# scale_factor +# Warnings: +# Wrong ConventionVersion +# Missing program value +# Missing programVersion value +# No time From 78e92d0eb4fa62ed73092e06914dc70874bd15da Mon Sep 17 00:00:00 2001 From: Irfan Date: Wed, 7 Aug 2019 16:17:12 +0100 Subject: [PATCH 10/38] More inpcrd changes and tests --- package/MDAnalysis/coordinates/INPCRD.py | 14 +- .../MDAnalysisTests/coordinates/test_ncrst.py | 325 +- .../data/Amber/ace_tip3p.ncrst | Bin 0 -> 101732 bytes .../data/Amber/ace_tip3p.parm7 | 2892 +++++++++++++++++ testsuite/MDAnalysisTests/datafiles.py | 5 +- 5 files changed, 3082 insertions(+), 154 deletions(-) create mode 100644 testsuite/MDAnalysisTests/data/Amber/ace_tip3p.ncrst create mode 100644 testsuite/MDAnalysisTests/data/Amber/ace_tip3p.parm7 diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index f76b95bb490..865a3b858f6 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -205,7 +205,7 @@ class NCRSTReader(base.SingleFrameReaderBase): units = {'time': 'ps', 'length': 'Angstrom', 'velocity': 'Angstrom/ps', - 'forces': 'kcal/(mol*Angstrom)'} + 'force': 'kcal/(mol*Angstrom)'} class Timestep(base.Timestep): """ Modified Timestep class for AMBER @@ -256,7 +256,7 @@ def _read_first_frame(self): "attribute Conventions)".format(self.filename)) logger.fatal(errmsg) raise TypeError(errmsg) - except KeyError: + except AttributeError: errmsg = "NetCDF file is missign Conventions" raise KeyError(errmsg) @@ -281,8 +281,8 @@ def _read_first_frame(self): try: # ConventionVersion should exist and be equal to 1.0 - if not rstfile.ConventionVersion.decode('utf-8') == - self.version: + if not (rstfile.ConventionVersion.decode('utf-8') == + self.version): wmsg = ("NCRST format is {0!s} but the reader implements " "format {1!s}".format( rstfile.ConventionVersion, self.version)) @@ -290,7 +290,7 @@ def _read_first_frame(self): logger.warning(wmsg) except KeyError: errmsg = "ConventionVersion not present in NetCDF file" - raise KeyError(errmsg) + raise AttributeError(errmsg) # The specs define Program and ProgramVersion as required. Here we # just warn the users instead of raising an Error. @@ -356,8 +356,8 @@ def _read_first_frame(self): self.ts.time = rstfile.variables['time'].getValue() except KeyError: # Warn the user and move on - wmsg = ("Restart file {0} does not contain time information. " - "This is should be expected if the file was not " + wmsg = ("NCRestart file {0} does not contain time information. " + "This should be expected if the file was not " "created from an MD trajectory (e.g. a " "minimization)".format(self.filename)) warnings.warn(wmsg) diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py index de3e0583f89..68aa54eb153 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -31,10 +31,7 @@ assert_almost_equal ) -from MDAnalysisTests.datafiles import (PFncdf_Top, PFncdf_Trj, - GRO, TRR, XYZ_mini) -from MDAnalysisTests.coordinates.reference import (RefVGV, RefTZ2) - +from MDAnalysisTests.datafiles import (PRMNCRSTbox, NCRSTbox) class _NCRestartTest(object): @@ -105,195 +102,231 @@ def test_has_forces(self, universe): assert_equal(self.has_forces, universe.trajectory.has_forces) -class Read_ACECFV(_NCRestartTest): +class TestReadACEBox(_NCRestartTest): """ACE in water with Coordinates, Forces and Velocities""" # Placeholder values - # topology = ACE - # filename = ACE-PARM7 + topology = PRMNCRSTbox + filename = NCRSTbox title = 'Cpptraj Generated Restart' n_atoms = 1398 n_res = 465 time = 1.0 has_velocities = True has_forces = True - - def test_positions(self, universe, selstr, expected): - ag = universe.select_atoms(selstr) + mmap = None + + def test_positions_resid1(self, universe): + ag = universe.select_atoms('resid 1') + expected = np.array([[16.91830635, 11.8711319, 15.46306515], + [16.02449417, 12.34413528, 15.86983871], + [16.05173683, 12.2475071, 16.95520592], + [15.09445763, 12.00988102, 15.41004944], + [16.09916306, 13.7953701, 15.57103825], + [16.00987625, 14.24524307, 14.39752007]], + dtype=np.float32) assert_almost_equal(expected, ag.positions, self.prec) - def test_velocities(self, universe, selstr, expected): - ag = universe.select_atoms(selstr) - assert_almost_equal(expected, ag.velocities, self.prec) + def test_positions_resid42(self, universe): + ag = universe.select_atoms('resid 42') + expected = np.array([[20.67843246, 21.18344688, 20.79789162], + [19.85808182, 21.5282135, 21.15058327], + [20.97104073, 20.54719162, 21.45041847]], + dtype=np.float32) + assert_almost_equal(expected, ag.positions, self.prec) - def test_forces(self, universe, selstr, expected): - ag = universe.select_atoms(selstr) - # We convert from kj back to the original kcal value - assert_almost_equal(expected, ag.forces * 4.184, self.prec) +# def test_velocities(self, universe, selstr, expected): +# ag = universe.select_atoms(selstr) +# assert_almost_equal(expected, ag.velocities, self.prec) +# +# def test_forces(self, universe, selstr, expected): +# ag = universe.select_atoms(selstr) +# # We convert from kj back to the original kcal value +# assert_almost_equal(expected, ag.forces * 4.184, self.prec) -class ExceptionsNCRSTGenerator(object): +class _NCRSTGenerator(object): """A basic modular ncrst writer based on :class:`NCDFWriter`""" - def create_ncrst(self): + def create_ncrst(self, params): # Create under context manager - with netcdf.netcdf_file(self.filename, mode='w', - version=self.version_byte) as ncrst: + with netcdf.netcdf_file(params['filename'], mode='w', + version=params['version_byte']) as ncrst: # Top level attributes - if self.Conventions: - setattr(ncrst, 'Conventions', self.Conventions) - if self.ConventionVersion: - setattr(ncrst, 'ConventionVersion', self.ConventionVersion) - if self.program: - setattr(ncrst, 'program', self.program) - if self.programVersion: - setattr(ncrst, 'programVersion', self.programVersion) + if params['Conventions']: + setattr(ncrst, 'Conventions', params['Conventions']) + if params['ConventionVersion']: + setattr(ncrst, 'ConventionVersion', + params['ConventionVersion']) + if params['program']: + setattr(ncrst, 'program', params['program']) + if params['programVersion']: + setattr(ncrst, 'programVersion', params['programVersion']) # Dimensions - if self.n_atoms: - ncrst.createDimension('atom', self.n_atoms) - if self.spatial: - ncrst.createDimension('spatial', self.spatial) + if params['n_atoms']: + ncrst.createDimension('atom', params['n_atoms']) + if params['spatial']: + ncrst.createDimension('spatial', params['spatial']) + if params['time']: + ncrst.createDimension('time', 1) # Variables - if self.time: - time = ncrst.createVariable('time', 'f8') - time = 1.0 - setattr(time, 'units', self.time) + if params['time']: + time = ncrst.createVariable('time', 'd', ('time',)) + setattr(time, 'units', params['time']) + time[:] = 1.0 # Spatial or atom dependent variables - if (self.spatial) and (self.n_atoms): - if self.coords: + if (params['spatial']) and (params['n_atoms']): + if params['coords']: coords = ncrst.createVariable('coordinates', 'f8', ('atom', 'spatial')) - setattr(coords, 'units', self.coords) - coords[:] = np.asarray(range(self.spatial), + setattr(coords, 'units', params['coords']) + coords[:] = np.asarray(range(params['spatial']), dtype=np.float32) spatial = ncrst.createVariable('spatial', 'c', ('spatial',)) - spatial[:] = np.asarray(list('xyz')) + spatial[:] = np.asarray(list('xyz')[:params['spatial']]) velocs = ncrst.createVariable('velocities', 'f8', ('atom', 'spatial')) setattr(velocs, 'units', 'angstrom/picosecond') - velocs[:] = np.asarray(range(self.spatial), dtype=np.float32) + velocs[:] = np.asarray(range(params['spatial']), + dtype=np.float32) forces = ncrst.createVariable('forces', 'f8', ('atom', 'spatial')) setattr(forces, 'units', 'kilocalorie/mole/angstrom') - forces[:] = np.asarray(range(self.spatial), dtype=np.float32) + forces[:] = np.asarray(range(params['spatial']), + dtype=np.float32) # self.scale_factor overrides which variable gets a scale_factor - if self.scale_factor: - setattr(ncrst.variables[self.scale_factor], + if params['scale_factor']: + setattr(ncrst.variables[params['scale_factor']], 'scale_factor', 2.0) - # Default definitions - filename = 'test.ncrst' - version_byte = 2 - Conventions = 'AMBERRESTART' - ConventionVersion = '1.0' - program = 'mda test_writer' - programVersion = 'V42' - n_atoms = 1 - spatial = 3 - coords = 'angstrom' - time = 'picosecond' - scale_factor = None - - -def TestNCRSTReaderExceptions(ExceptionsNCRSTGenerator): - - # TO DO: merge these so you get TypeErrors, KeyErrors, etc... - - def test_VersionbyteError(self, tmpdir): - self.version_byte = 1 + def gen_params(self, key=None, value=None): + """Generate writer parameters, key and value can be used to overwrite + a given dictionary entry + """ + + params = { + 'filename': 'test.ncrst', + 'version_byte': 2, + 'Conventions': 'AMBERRESTART', + 'ConventionVersion': '1.0', + 'program': 'mda test_writer', + 'programVersion': 'V42', + 'n_atoms': 1, + 'spatial': 3, + 'coords': 'angstrom', + 'time': 'picosecond', + 'scale_factor': None + } + + if key: + params[key] = value + + return params + + +class TestNCRSTReaderExceptionsWarnings(_NCRSTGenerator): + + @pytest.mark.parametrize('key,value', ( + ('version_byte', 1), + ('Conventions', 'Foo'), + ('spatial', 2) + )) + def test_read_type_errors(self, tmpdir, key, value): + params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): - self.create_ncrst() + self.create_ncrst(params) with pytest.raises(TypeError): - NCRSTReader(self.filename) - - def test_WrongConventionsError(self, tmpdir): - self.Conventions = 'Foo' + NCRSTReader(params['filename']) + + @pytest.mark.parametrize('key,value', ( + ('Conventions', None), + ('ConventionVersion', None) + )) + def test_attribute_errors(self, tmpdir, key, value): + params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(TypeError): - NCRSTReader(self.filename) - - def test_NoConventionsError(self, tmpdir): - self.Conventions = None + self.create_ncrst(params) + with pytest.raises(AttributeError): + NCRSTReader(params['filename']) + + @pytest.mark.parametrize('key,value', ( + ('spatial', None), + ('n_atoms', None), + ('coords', None) + )) + def test_key_errors(self, tmpdir, key, value): + params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): - self.create_ncrst() + self.create_ncrst(params) with pytest.raises(KeyError): - NCRSTReader(self.filename) - - def test_WrongConventionVersionError(self, tmpdir): - self.ConventionVersion = '2.0' - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(TypeError): - NCRSTReader(self.filename) - - def test_NoConventionVersionError(self, tmpdir): - self.ConventionVersion = None + NCRSTReader(params['filename']) + + @pytest.mark.parametrize('key,value', ( + ('time', 'femtosecond'), + ('coords', 'nanometer') + )) + def test_not_implemented_errors(self, tmpdir, key, value): + params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(KeyError): - NCRSTReader(self.filename) - - def test_WrongSpatialError(self, tmpdir): - self.spatial = 2 - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(TypeError): - NCRSTReader(self.filename) - - def test_NoSpatialError(self, tmpdir): - self.spatial = None - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(KeyError): - NCRSTReader(self.filename) - - def test_NoAtomsError(self, tmpdir): - self.n_atoms = None - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(KeyError): - NCRSTReader(self.filename) - - def test_WrongTimeError(self, tmpdir): - self.time = 'femtosecond' - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(NotImplementedError): - NCRSTReader(self.filename) - - def test_WrongCoordsError(self, tmpdir): - self.coords = 'nanometer' - with tmpdir.as_cwd(): - self.create_ncrst() + self.create_ncrst(params) with pytest.raises(NotImplementedError): - NCRSTReader(self.filename) - - def test_NoCoordsError(self, tmpdir): - self.coords = None - with tmpdir.as_cwd(): - self.create_ncrst() - with pytest.raises(KeyError): - NCRSTReader(self.filename) + NCRSTReader(params['filename']) - @pytest.mark.parametrize('variable', [ + @pytest.mark.parametrize('value', [ 'time', 'coordinates', 'spatial', 'velocities', 'forces' ]) - def test_scale_factor(self, tmpdir, variable): - self.scale_factor = variable + def test_scale_factor(self, tmpdir, value): + params = self.gen_params(key='scale_factor', value=value) with tmpdir.as_cwd(): - self.create_ncrst() + self.create_ncrst(params) with pytest.raises(NotImplementedError): - NCRSTReader(self.filename) - -# Errors: -# scale_factor -# Warnings: -# Wrong ConventionVersion -# Missing program value -# Missing programVersion value -# No time + NCRSTReader(params['filename']) + + def test_conventionversion_warn(self, tmpdir): + params = self.gen_params(key='ConventionVersion', value='2.0') + with tmpdir.as_cwd(): + self.create_ncrst(params) + with pytest.warns(UserWarning) as record: + NCRSTReader(params['filename']) + + assert len(record) == 1 + wmsg = "NCRST format is 2.0 but the reader implements format 1.0" + assert str(record[0].message.args[0]) == wmsg + + @pytest.mark.parametrize('key,value', ( + ('program', None), + ('programVersion', None) + )) + def test_program_warn(self, tmpdir, key, value): + params = self.gen_params(key=key, value=value) + with tmpdir.as_cwd(): + self.create_ncrst(params) + with pytest.warns(UserWarning) as record: + NCRSTReader(params['filename']) + + assert len(record) == 1 + wmsg = ("This NCRST file may not fully adhere to AMBER " + "standards as either the `program` or `programVersion` " + "attributes are missing") + assert str(record[0].message.args[0]) == wmsg + + def test_notime_warn(self, tmpdir): + params = self.gen_params(key='time', value=None) + with tmpdir.as_cwd(): + self.create_ncrst(params) + with pytest.warns(UserWarning) as record: + NCRSTReader(params['filename']) + + # Lack of time triggers two warnings + assert len(record) == 2 + wmsg1 = ("NCRestart file {0} does not contain time information. 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+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 +%FLAG IPOL +%FORMAT(1I8) + 0 diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 67d5824cb01..db0d141f039 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -95,7 +95,8 @@ "PRMncdf", "TRJncdf", "NCDF", # Amber (netcdf) "PFncdf_Top", "PFncdf_Trj", # Amber ncdf with Positions and Forces "PRMcs", # Amber (format, Issue 1331) - "PRMNCRST", # Amber ncrst with positions/forces/velocities + "PRMNCRST", # Amber topology for ACE in gas phase + "PRMNCRSTbox", "NCRSTbox", # Amber: ACE in tip3p w/ coords, vels, forces, and box dimensions "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) "PRMErr1", "PRMErr2", "PRMErr3", # Amber TOP files to check raised errors "PQR", # PQR v1 @@ -345,6 +346,8 @@ PRMcs = resource_filename(__name__, 'data/Amber/chitosan.prmtop') PRMNCRST = resource_filename(__name__, 'data/Amber/ace_mbondi3.parm7') +PRMNCRSTbox = resource_filename(__name__, 'data/Amber/ace_tip3p.parm7') +NCRSTbox = resource_filename(__name__, 'data/Amber/ace_tip3p.ncrst') PRMNEGATIVE = resource_filename(__name__, 'data/Amber/ace_mbondi3.negative.parm7') From 474ab59b67f52d2f62f6ad02862293e488ff0334 Mon Sep 17 00:00:00 2001 From: Irfan Date: Wed, 7 Aug 2019 16:19:25 +0100 Subject: [PATCH 11/38] Error type change --- package/MDAnalysis/coordinates/INPCRD.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 865a3b858f6..b8102c1bb63 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -258,7 +258,7 @@ def _read_first_frame(self): raise TypeError(errmsg) except AttributeError: errmsg = "NetCDF file is missign Conventions" - raise KeyError(errmsg) + raise AttributeError(errmsg) # The AMBER NetCDF standard enforces 64 bit offsets if not rstfile.version_byte == 2: @@ -285,7 +285,8 @@ def _read_first_frame(self): self.version): wmsg = ("NCRST format is {0!s} but the reader implements " "format {1!s}".format( - rstfile.ConventionVersion, self.version)) + rstfile.ConventionVersion.decode('utf-8'), + self.version)) warnings.warn(wmsg) logger.warning(wmsg) except KeyError: @@ -294,7 +295,7 @@ def _read_first_frame(self): # The specs define Program and ProgramVersion as required. Here we # just warn the users instead of raising an Error. - if not (hasattr(rstfile, 'program') or + if not (hasattr(rstfile, 'program') and hasattr(rstfile, 'programVersion')): wmsg = ("This NCRST file may not fully adhere to AMBER " "standards as either the `program` or " From e5d7cb611bb2fad79755f00450df431f7755d5e7 Mon Sep 17 00:00:00 2001 From: Irfan Date: Fri, 16 Aug 2019 22:33:38 +0100 Subject: [PATCH 12/38] Changes to match initial PR 2326 --- package/MDAnalysis/coordinates/INPCRD.py | 139 +++++++++++++---------- 1 file changed, 81 insertions(+), 58 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index b8102c1bb63..d0aa519466b 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -154,9 +154,8 @@ class NCRSTReader(base.SingleFrameReaderBase): The number of atoms (`n_atoms`) does not have to be provided as it can be read from the input NETCDF file. - Current simulation time is autodetected and read into the - :attr:`Timestep.time` attribute. (If this is not available in the restart - file, then :attr:`Timestep.time` will return 0.0 ps). + Current simulation time is autodetected and if available is read into the + :attr:`Timestep.time` attribute. Velocities are autodetected and read into the :attr:`Timestep._velocities` attribute. @@ -184,8 +183,8 @@ class NCRSTReader(base.SingleFrameReaderBase): .. rubric:: Limitations - * Only NCRST files with time in ps and lengths in Angstroem are processed. - * scale_factors are not supported (raises NotImplementedError). + * Only NCRST files with time in ps, lengths in Angstroem and angles in + degree are processed. * Restart files without coordinate information are not supported. * Replica exchange variables are not supported. @@ -233,6 +232,14 @@ def parse_n_atoms(filename, **kwargs): n_atoms = f.dimensions['atom'] return n_atoms + @staticmethod + def verify_units(eval_units, expected_units): + if eval_units.decode('utf-8') not in expected_units: + errmsg = ("NCRSTReader currently assumes that the trajectory " + "aws written in units of {0} instead of {1}".format( + expected_units, eval_units.decode('utf-8'))) + raise NotImplementedError(errmsg) + def _read_first_frame(self): """Function to read NetCDF restart file and fill timestep @@ -257,13 +264,27 @@ def _read_first_frame(self): logger.fatal(errmsg) raise TypeError(errmsg) except AttributeError: - errmsg = "NetCDF file is missign Conventions" + errmsg = "NetCDF file is missing Conventions" + raise AttributeError(errmsg) + + # ConventionVersion should exist and be equal to 1.0 + try: + if not (rstfile.ConventionVersion.decode('utf-8') == + self.version): + wmsg = ("NCRST format is {0!s} but the reader implements " + "format {1!s}".format( + rstfile.ConventionVersion.decode('utf-8'), + self.version)) + warnings.warn(wmsg) + logger.warning(wmsg) + except KeyError: + errmsg = "ConventionVersion not present in NetCDF file" raise AttributeError(errmsg) # The AMBER NetCDF standard enforces 64 bit offsets if not rstfile.version_byte == 2: errmsg = ("NetCDF restart file {0} does not conform to AMBER " - "specifications, as details in " + "specifications, as detailed in " "http://ambermd.org/netcdf/nctraj.xhtml " "(NetCDF file does not use 64 bit offsets " "[version_byte = 2]) ".format(self.filename)) @@ -276,24 +297,10 @@ def _read_first_frame(self): errmsg = "Incorrect spatial value for NCRST file" raise TypeError(errmsg) except KeyError: - errmsg = "NCRST file does not contain sptial dimension" + errmsg = "NCRST file does not contain spatial dimension" raise KeyError(errmsg) - try: - # ConventionVersion should exist and be equal to 1.0 - if not (rstfile.ConventionVersion.decode('utf-8') == - self.version): - wmsg = ("NCRST format is {0!s} but the reader implements " - "format {1!s}".format( - rstfile.ConventionVersion.decode('utf-8'), - self.version)) - warnings.warn(wmsg) - logger.warning(wmsg) - except KeyError: - errmsg = "ConventionVersion not present in NetCDF file" - raise AttributeError(errmsg) - - # The specs define Program and ProgramVersion as required. Here we + # The specs define program and programVersion as required. Here we # just warn the users instead of raising an Error. if not (hasattr(rstfile, 'program') and hasattr(rstfile, 'programVersion')): @@ -303,13 +310,6 @@ def _read_first_frame(self): warnings.warn(wmsg) logger.warning(wmsg) - # The use of scale_factor is currently unsupported - # Note scale_factor can be an attribute of any variable - for variable in rstfile.variables: - if hasattr(rstfile.variables[variable], 'scale_factor'): - errmsg = "scale_factors are not implemented" - raise NotImplementedError(errmsg) - # Note: SingleFrameReaderBase class sets parsed n_atoms value to # self.n_atom which makes for a confusing check try: @@ -326,6 +326,12 @@ def _read_first_frame(self): logger.fatal(errmsg) raise KeyError(errmsg) + # NetCDF file title is optional + try: + self.remarks = rstfile.title + except AttributeError: + self.remarks = "" + # Optional variables self.has_velocities = 'velocities' in rstfile.variables self.has_forces = 'forces' in rstfile.variables @@ -338,28 +344,36 @@ def _read_first_frame(self): reader=self, **self._ts_kwargs) - # NetCDF file title is optional - try: - self.remarks = rstfile.title - except AttributeError: - self.remarks = "" + # Check for scale_factor attributes and store them + scale_factors = {'time': 1.0, + 'cell_lengths': 1.0, + 'cell_angles': 1.0, + 'coordinates': 1.0, + 'velocities': 1.0, + 'forces': 1.0} + + for variable in rstfile.variables: + if hasattr(rstfile.variables[variable], 'scale_factor'): + if variable in scale_factors: + factor = rstfile.variables[variable].scale_factor + scale_factors[variable] = factor + else: + errmsg = ("scale_factors for variable {0} are not " + "implemented".format(variable)) + raise NotImplementedError(errmsg) - # Default to time units of picoseconds # Note: unlike trajectories the AMBER NetCDF convention allows # restart files to omit time when unecessary (i.e. minimizations) try: - units = rstfile.variables['time'].units.decode('utf-8') - if units != "picosecond": - raise NotImplementedError( - "NCRSTReader currently assumes that the restart file " - "uses a time unit of picoseconds and not {0}.".format( - rstfile.variables['time'].units)) - self.ts.time = rstfile.variables['time'].getValue() + self.verify_units(rstfile.variables['time'].units, + ('picosecond',)) + self.ts.time = (rstfile.variables['time'].getValue() * + scale_factors['time']) except KeyError: # Warn the user and move on - wmsg = ("NCRestart file {0} does not contain time information. " - "This should be expected if the file was not " - "created from an MD trajectory (e.g. a " + wmsg = ("NCRestart file {0} does not contain time " + "information. This should be expected if the file was " + "not created from an MD trajectory (e.g. a " "minimization)".format(self.filename)) warnings.warn(wmsg) logger.warning(wmsg) @@ -367,15 +381,12 @@ def _read_first_frame(self): # Single frame so we assign it to 0 self.ts.frame = 0 - # Default to length units of Angstroem + # Default to length units of Angstrom try: - units = rstfile.variables['coordinates'].units.decode('utf-8') - if units != "angstrom": - raise NotImplementedError( - "NCRSTReader currently expects that the restart file " - "uses a length unit of Angstroem and not {0}.".format( - rstfile.variables['coordinates'].units)) - self.ts._pos[:] = rstfile.variables['coordinates'][:] + self.verify_units(rstfile.variables['coordinates'].units, + ('angstrom',)) + self.ts._pos[:] = (rstfile.variables['coordinates'][:] * + scale_factors['coordinates']) except KeyError: # Technically coordinate information is not required, however # the lack of it in a restart file is highly unlikely @@ -385,17 +396,29 @@ def _read_first_frame(self): raise KeyError(errmsg) if self.has_velocities: - self.ts._velocities[:] = rstfile.variables['velocities'][:] + self.verify_units(rstfile.variables['velocities'].units, + ('angstrom/picosecond',)) + self.ts._velocities[:] = (rstfile.variables['velocities'][:] * + scale_factors['velocities']) # The presence of forces in a restart file is very rare, but # according to AMBER convention, it can exist. if self.has_forces: - self.ts._forces[:] = rstfile.variables['forces'][:] + self.verify_units(rstfile.variables['forces'].units, + ('kilocalorie/mole/angstrom',)) + self.ts._forces[:] = (rstfile.variables['forces'][:] * + scale_factors['forces']) # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] if self.periodic: - self.ts._unitcell[:3] = rstfile.variables['cell_lengths'][:] - self.ts._unitcell[3:] = rstfile.variables['cell_angles'][:] + self.verify_units(rstfile.variables['cell_lengths'].units, + ('angstrom',)) + self.verify_units(rstfile.variables['cell_angles'].units, + ('degree', 'degrees')) + self.ts._unitcell[:3] = (rstfile.variables['cell_lengths'][:] * + scale_factors['cell_lengths']) + self.ts._unitcell[3:] = (rstfile.variables['cell_angles'][:] * + scale_factors['cell_angles']) # Convert units inplace if self.convert_units: From 2554ff0b713de19cf99e504c9958e81b64fef89f Mon Sep 17 00:00:00 2001 From: Irfan Date: Mon, 19 Aug 2019 18:52:16 +0100 Subject: [PATCH 13/38] Swapping to ValueErrors --- package/MDAnalysis/coordinates/INPCRD.py | 53 +++++++++++++----------- 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index d0aa519466b..6c6556a6bf2 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -101,6 +101,9 @@ class INPReader(base.SingleFrameReaderBase): * Box information is not read (or checked for). * Velocities are currently *not supported*. + .. versionchanged: 0.20.0 + Now automatically detects files with .rst7 extension. + """ format = ['INPCRD', 'RESTRT', 'RST7'] @@ -233,11 +236,11 @@ def parse_n_atoms(filename, **kwargs): return n_atoms @staticmethod - def verify_units(eval_units, expected_units): - if eval_units.decode('utf-8') not in expected_units: + def _verify_units(eval_units, expected_units): + if eval_units.decode('utf-8') != expected_units: errmsg = ("NCRSTReader currently assumes that the trajectory " - "aws written in units of {0} instead of {1}".format( - expected_units, eval_units.decode('utf-8'))) + "was written in units of {0} instead of {1}".format( + eval_units.decode('utf-8'), expected_units)) raise NotImplementedError(errmsg) def _read_first_frame(self): @@ -249,13 +252,11 @@ def _read_first_frame(self): # Open netcdf file via context manager with scipy.io.netcdf.netcdf_file(self.filename, mode='r', mmap=self._mmap) as rstfile: - # Global attribute checks - # Conventions should contain the AMBERRESTART string + # Conventions should exist and contain the AMBERRESTART string try: - if not ('AMBERRESTART' in - rstfile.Conventions.decode('utf-8').split(',') or - 'AMBERRESTART' in - rstfile.Conventions.decode('utf-8').split()): + conventions = rstfile.Conventions.decode('utf-8') + if not ('AMBERRESTART' in conventions.split(',') or + 'AMBERRESTART' in conventions.split()): errmsg = ("NetCDF restart file {0} does not conform to " "AMBER specifications, as detailed in " "http://ambermd.org/netcdf/nctraj.xhtml " @@ -264,22 +265,24 @@ def _read_first_frame(self): logger.fatal(errmsg) raise TypeError(errmsg) except AttributeError: - errmsg = "NetCDF file is missing Conventions" - raise AttributeError(errmsg) + errmsg = ("NetCDF restart file {0} is missing a " + "Conventions value".format(self.filename)) + raise ValueError(errmsg) # ConventionVersion should exist and be equal to 1.0 try: - if not (rstfile.ConventionVersion.decode('utf-8') == - self.version): + ConventionVersion = rstfile.ConventionVersion.decode('utf-8') + if not (ConventionVersion == self.version): wmsg = ("NCRST format is {0!s} but the reader implements " "format {1!s}".format( rstfile.ConventionVersion.decode('utf-8'), self.version)) warnings.warn(wmsg) logger.warning(wmsg) - except KeyError: - errmsg = "ConventionVersion not present in NetCDF file" - raise AttributeError(errmsg) + except AttributeError: + errmsg = ("NCDF restart file {0} is missing a " + "ConventionVersion value".format(self.filename)) + raise ValueError(errmsg) # The AMBER NetCDF standard enforces 64 bit offsets if not rstfile.version_byte == 2: @@ -297,16 +300,18 @@ def _read_first_frame(self): errmsg = "Incorrect spatial value for NCRST file" raise TypeError(errmsg) except KeyError: - errmsg = "NCRST file does not contain spatial dimension" - raise KeyError(errmsg) + errmsg = ("NCDF restart file {0} does not contain spatial " + "dimension".format(self.filename)) + raise ValueError(errmsg) # The specs define program and programVersion as required. Here we # just warn the users instead of raising an Error. if not (hasattr(rstfile, 'program') and hasattr(rstfile, 'programVersion')): - wmsg = ("This NCRST file may not fully adhere to AMBER " + wmsg = ("This NCRST file {0} may not fully adhere to AMBER " "standards as either the `program` or " - "`programVersion` attributes are missing") + "`programVersion` attributes are missing".format( + self.filename)) warnings.warn(wmsg) logger.warning(wmsg) @@ -324,7 +329,7 @@ def _read_first_frame(self): errmsg = ("NetCDF restart file {0} does not contain " "atom information ".format(self.filename)) logger.fatal(errmsg) - raise KeyError(errmsg) + raise ValueError(errmsg) # NetCDF file title is optional try: @@ -365,8 +370,8 @@ def _read_first_frame(self): # Note: unlike trajectories the AMBER NetCDF convention allows # restart files to omit time when unecessary (i.e. minimizations) try: - self.verify_units(rstfile.variables['time'].units, - ('picosecond',)) + self._verify_units(rstfile.variables['time'].units, + 'picosecond') self.ts.time = (rstfile.variables['time'].getValue() * scale_factors['time']) except KeyError: From 8cc8161d148bf594c6d3b309ae00fe7a2c864d34 Mon Sep 17 00:00:00 2001 From: Irfan Date: Mon, 19 Aug 2019 19:24:07 +0100 Subject: [PATCH 14/38] Update _verify_units and typos --- package/MDAnalysis/coordinates/INPCRD.py | 29 ++++++++++++------------ 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 6c6556a6bf2..34712d4368c 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -274,8 +274,7 @@ def _read_first_frame(self): ConventionVersion = rstfile.ConventionVersion.decode('utf-8') if not (ConventionVersion == self.version): wmsg = ("NCRST format is {0!s} but the reader implements " - "format {1!s}".format( - rstfile.ConventionVersion.decode('utf-8'), + "format {1!s}".format(ConventionVersion, self.version)) warnings.warn(wmsg) logger.warning(wmsg) @@ -388,8 +387,8 @@ def _read_first_frame(self): # Default to length units of Angstrom try: - self.verify_units(rstfile.variables['coordinates'].units, - ('angstrom',)) + self._verify_units(rstfile.variables['coordinates'].units, + 'angstrom') self.ts._pos[:] = (rstfile.variables['coordinates'][:] * scale_factors['coordinates']) except KeyError: @@ -398,28 +397,28 @@ def _read_first_frame(self): errmsg = ("NetCDF restart file {0} is missing coordinate " "information ".format(self.filename)) logger.fatal(errmsg) - raise KeyError(errmsg) + raise ValueError(errmsg) if self.has_velocities: - self.verify_units(rstfile.variables['velocities'].units, - ('angstrom/picosecond',)) + self._verify_units(rstfile.variables['velocities'].units, + 'angstrom/picosecond') self.ts._velocities[:] = (rstfile.variables['velocities'][:] * scale_factors['velocities']) - # The presence of forces in a restart file is very rare, but - # according to AMBER convention, it can exist. + # The presence of forces in an ncrst is rare but possible if self.has_forces: - self.verify_units(rstfile.variables['forces'].units, - ('kilocalorie/mole/angstrom',)) + self._verify_units(rstfile.variables['forces'].units, + 'kilocalorie/mole/angstrom') self.ts._forces[:] = (rstfile.variables['forces'][:] * scale_factors['forces']) # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] + # Unlike the NCDFReader, `degrees` is not accepted if self.periodic: - self.verify_units(rstfile.variables['cell_lengths'].units, - ('angstrom',)) - self.verify_units(rstfile.variables['cell_angles'].units, - ('degree', 'degrees')) + self._verify_units(rstfile.variables['cell_lengths'].units, + 'angstrom') + self._verify_units(rstfile.variables['cell_angles'].units, + 'degree') self.ts._unitcell[:3] = (rstfile.variables['cell_lengths'][:] * scale_factors['cell_lengths']) self.ts._unitcell[3:] = (rstfile.variables['cell_angles'][:] * From bcc58c8bd6d8501353e3fe981da8629d276ae757 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 30 Nov 2022 13:39:21 +0000 Subject: [PATCH 15/38] Update INPCRD.py --- package/MDAnalysis/coordinates/INPCRD.py | 23 ++++++----------------- 1 file changed, 6 insertions(+), 17 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index a0640b73904..42eb43f8366 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -87,6 +87,10 @@ import warnings import logging +from .timestep import Timestep +from ..lib.util import store_init_arguments + + logger = logging.getLogger("MDAnalysis.coordinates.AMBER") @@ -168,9 +172,6 @@ class NCRSTReader(base.SingleFrameReaderBase): the restart file, then :attr:`Timestep.dimensions` will return ``[0,0,0,0,0,0]``). - The NCRST reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` - must be installed. - Support for the *mmap* keyword is available as detailed in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. The use of ``mmap=True`` leads to around a 2x read speed improvement in a ~ 1 million @@ -195,8 +196,8 @@ class NCRSTReader(base.SingleFrameReaderBase): :class:`NCDFReader` :class:`NCDFWriter` - .. versionadded: 0.20.0 + .. versionadded: 2.5.0 """ format = ['NCRST', 'NCRESTRT', 'NCRST7'] @@ -206,19 +207,10 @@ class NCRSTReader(base.SingleFrameReaderBase): 'velocity': 'Angstrom/ps', 'force': 'kcal/(mol*Angstrom)'} - class Timestep(base.Timestep): - """ Modified Timestep class for AMBER - - Uses C order memory mapping to match the style used by AMBER TRAJ - - The Timestep can be initialized with `arg` being an integer - (the number of atoms) and an optional keyword arguments to allocate - space for velocities, and forces. - """ - order = 'C' _Timestep = Timestep + @store_init_arguments def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs): # Assign input mmap value @@ -242,9 +234,6 @@ def _verify_units(eval_units, expected_units): def _read_first_frame(self): """Function to read NetCDF restart file and fill timestep - - Called by: :class:`SingleFrameReaderBase`.__init__ - Overrides :class:`SingleFrameReaderBase` placeholder function """ # Open netcdf file via context manager with scipy.io.netcdf.netcdf_file(self.filename, mode='r', From 30a2b121e3f063dc2cc11944ffac4121b693c0c4 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Wed, 16 Apr 2025 17:33:57 -0400 Subject: [PATCH 16/38] working commit --- package/MDAnalysis/coordinates/TRJ.py | 47 +++++++++++++++++++-------- 1 file changed, 33 insertions(+), 14 deletions(-) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index e9799e4d945..04f92e57f84 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -359,7 +359,7 @@ class NCDFReader(base.ReaderBase): """Reader for `AMBER NETCDF format`_ (version 1.0). AMBER binary trajectories are automatically recognised by the - file extension ".ncdf". + file extension ".ncdf", ".nc", and '.ncrst'. The number of atoms (`n_atoms`) does not have to be provided as it can be read from the trajectory. The trajectory reader can randomly access @@ -422,10 +422,12 @@ class NCDFReader(base.ReaderBase): the first two frames of the trajectory. :meth:`Writer` now also sets `convert_units`, `velocities`, `forces` and `scale_factor` information for the :class:`NCDFWriter`. + .. versionchanged:: 2.10.0 + Now reads `AMBERRESTART` convention `.ncrst` files. """ - format = ['NCDF', 'NC'] + format = ['NCDF', 'NC', 'NCRST'] multiframe = True version = "1.0" units = {'time': 'ps', @@ -450,8 +452,14 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): # AMBER NetCDF files should always have a convention try: conventions = self.trjfile.Conventions - if not ('AMBER' in conventions.decode('utf-8').split(',') or - 'AMBER' in conventions.decode('utf-8').split()): + check = [conventions.decode('utf-8').split(','), + conventions.decode('utf-8').split()] + + if 'AMBER' in check[0] or 'AMBER' in check[1]: + self.is_restart = False + elif 'AMBERRESTART' in check[0] or 'AMBERRESTART' in check[1]: + self.is_restart = True + else: errmsg = ("NCDF trajectory {0} does not conform to AMBER " "specifications, " "http://ambermd.org/netcdf/nctraj.xhtml " @@ -530,9 +538,12 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): if self.n_frames is None: self.n_frames = self.trjfile.variables['coordinates'].shape[0] except KeyError: - errmsg = (f"NCDF trajectory {self.filename} does not contain " - f"frame information") - raise ValueError(errmsg) from None + if self.is_restart: + self.n_frames = 1 + else: + errmsg = (f"NCDF trajectory {self.filename} does not contain " + f"frame information") + raise ValueError(errmsg) from None try: self.remarks = self.trjfile.title @@ -645,21 +656,27 @@ def _read_frame(self, frame): if np.dtype(type(frame)) != np.dtype(int): # convention... for netcdf could also be a slice raise TypeError("frame must be a positive integer or zero") - if frame >= self.n_frames or frame < 0: + if (frame >= self.n_frames or frame < 0): raise IndexError("frame index must be 0 <= frame < {0}".format( self.n_frames)) # note: self.trjfile.variables['coordinates'].shape == (frames, n_atoms, 3) - ts._pos[:] = self._get_var_and_scale('coordinates', frame) + + if self.is_restart: + check_frame = () # AMBERRESTART convention files have dimensionless datasets + else: + check_frame = int(frame) + + ts._pos[:] = self._get_var_and_scale('coordinates', check_frame) if self.has_time: - ts.time = self._get_var_and_scale('time', frame) + ts.time = self._get_var_and_scale('time', check_frame) if self.has_velocities: - ts._velocities[:] = self._get_var_and_scale('velocities', frame) + ts._velocities[:] = self._get_var_and_scale('velocities', check_frame) if self.has_forces: - ts._forces[:] = self._get_var_and_scale('forces', frame) + ts._forces[:] = self._get_var_and_scale('forces', check_frame) if self.periodic: unitcell = np.zeros(6) - unitcell[:3] = self._get_var_and_scale('cell_lengths', frame) - unitcell[3:] = self._get_var_and_scale('cell_angles', frame) + unitcell[:3] = self._get_var_and_scale('cell_lengths', check_frame) + unitcell[3:] = self._get_var_and_scale('cell_angles', check_frame) ts.dimensions = unitcell if self.convert_units: self.convert_pos_from_native(ts._pos) # in-place ! @@ -673,6 +690,8 @@ def _read_frame(self, frame): if self.periodic: # in-place ! (only lengths) self.convert_pos_from_native(ts.dimensions[:3]) + + del check_frame ts.frame = frame # frame labels are 0-based self._current_frame = frame return ts From e2e04553ea31526b3472440fe498ead1ec34b13d Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 17 Apr 2025 00:22:27 -0400 Subject: [PATCH 17/38] test for NCRST --- .../coordinates/test_netcdf.py | 68 ++++++++++++++++++ .../data/Amber/ace_mbondi3.ncrst | Bin 0 -> 1132 bytes testsuite/MDAnalysisTests/datafiles.py | 4 +- 3 files changed, 71 insertions(+), 1 deletion(-) create mode 100644 testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.ncrst diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index 1ebad11665c..ef1b2f9d3a6 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -41,6 +41,8 @@ DLP_CONFIG, CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ, + PRMNCRST, + TRJNCRST, ) from MDAnalysisTests.coordinates.test_trj import _TRJReaderTest from MDAnalysisTests.coordinates.reference import RefVGV, RefTZ2 @@ -389,6 +391,72 @@ def test_warn_user_no_time_information(self, u): u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) +class TestNCDFReader5(object): + """NCRST Restart File with positions and forces, exported by CPPTRAJ. + + Contributed by Jeremy M. G. Leung + """ + + prec = 6 + + @pytest.fixture(scope="class") + def u(self): + return mda.Universe(PRMNCRST, TRJNCRST) + + def test_positions(self, u): + """Check positions on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [-1.1455358, -2.0177484, -0.55771565], + [-0.19042611, -2.2511053, -1.0282656], + [ 0.53238064, -1.5778863, -0.56737846], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec) + + def test_velocities(self, u): + """Check forces on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [11.86471367, 31.22108269, -4.03538418], + [7.36676359, -4.68035316, 1.78124952], + [12.86675262, 1.39324546, -14.97190762], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec) + + def test_forces(self, u): + """Check forces on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [-9.7262249, -0.37627634, -24.79876137], + [-32.43384552, 37.47783279, -12.45422745], + [24.10939026, -19.80618095, -17.09523582], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec) + + def test_time(self, u): + """Check time on first frame""" + ref = 5.0 + assert_almost_equal(ref, u.trajectory[0].time, self.prec) + + def test_dt(self, u): + """Default 1.0 fs""" + ref = 1.0 + assert_almost_equal(ref, u.trajectory.dt, self.prec) + assert_almost_equal(ref, u.trajectory.ts.dt, self.prec) + + def test_box(self, u): + assert u.trajectory[0].dimensions is None + + class _NCDFGenerator(object): """A class for generating abitrary ncdf files and exhaustively test edge cases which might not be found in the wild""" diff --git a/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.ncrst b/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.ncrst new file mode 100644 index 0000000000000000000000000000000000000000..9639b16fb289cffe6542d39cb96e90557244d51f GIT binary patch literal 1132 zcmZ{iT}TvB6vyxGy7{qFloetTZXhHDYf4|x!;Fo#^!2i-6$tJyjy5^YU1n}lLNGZz${W2?Ex-VIjsaXosI^rqKW{SnU zBP6C|GKQ{#FE#Tq(S`%Nno|Dv;*3SRECti}HK@KH>Se*VR?V`5aQ{r}wnW{IL>-=q z$<*xCOtiOAV@-nRpK3bT+>mMpz2eWALM!iVq%N@;<6#@)e^Z(n=%Di9g-;D{jsu)^(r=l`yK^(q=khF#M zO(h3b1vlVkGP+k z*QH_2N%av4=uS;Mc90L+rvZeA!?LI6?2#;JajH~~1Kl5Dlq07%e9a+8tL7yj56LrW zB$>I26h~fj0O3p9yhrAKH16Ss`z~_U0rGM|K)Q2lPH~_(eSR>D{NDXC4s;(%rybNU zgnmzt?HS^zZ}0sEAmW?&yr*x_=ULG1dt-GRC{7Mu1`zklxc3;`{^Wg*`xB%siyUsf z1|Z_yn`=4p$9H18zs=c0dUIuM*si- literal 0 HcmV?d00001 diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 7cdd9166ecd..68163438aec 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -191,7 +191,8 @@ "CPPTRAJ_TRAJ_TOP", "CPPTRAJ_TRAJ", # Amber ncdf extracted from CPPTRAJ without time variable "PRMcs", # Amber (format, Issue 1331) - "PRMNCRST", # Amber ncrst with positions/forces/velocities + "PRMNCRST", # Amber topology for ncrst with positions/forces/velocities + "TRJNCRST", # Amber ncrst with positions/forces/velocties "PRM_NCBOX", "TRJ_NCBOX", # Amber parm7 + nc w/ pos/forces/vels/box "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) @@ -662,6 +663,7 @@ PRMcs = (_data_ref / "Amber/chitosan.prmtop").as_posix() PRMNCRST = (_data_ref / "Amber/ace_mbondi3.parm7").as_posix() +TRJNCRST = (_data_ref / "Amber/ace_mbondi3.ncrst").as_posix() PRM_NCBOX = (_data_ref / "Amber/ace_tip3p.parm7").as_posix() TRJ_NCBOX = (_data_ref / "Amber/ace_tip3p.nc").as_posix() From d6627c7bf5a6285ae5cad22ac664c20755f04b16 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 17 Apr 2025 10:50:22 -0400 Subject: [PATCH 18/38] changelog + authors --- package/AUTHORS | 1 + package/CHANGELOG | 4 +++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/package/AUTHORS b/package/AUTHORS index 2d9b0190e81..e2e5a31d774 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -256,6 +256,7 @@ Chronological list of authors - James Rowe - Debasish Mohanty - Abdulrahman Elbanna + - Jeremy M.G. Leung External code diff --git a/package/CHANGELOG b/package/CHANGELOG index 35d673727fe..acfb9a8003e 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -15,7 +15,7 @@ The rules for this file: ------------------------------------------------------------------------------- ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev, - yuxuanzhuang, yuyuan871111 + yuxuanzhuang, yuyuan871111, jpkrowe, jeremyleung521 * 2.10.0 @@ -31,6 +31,8 @@ Fixes (Issue #4948, PR #5001) Enhancements + * Allow NCDF reader to read Amber Restart Files with extension `.ncrst` + (Issue #5030, PR#5031) * Improve parsing of topology information from LAMMPS dump files to allow reading of mass, charge and element attributes. (Issue #3449, PR #4995) * Added timestep support for XDR writers and readers (Issue #4905, PR #4908) From fb0d2e9a926baff9aca6178f83256947920b9719 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 17 Apr 2025 11:01:56 -0400 Subject: [PATCH 19/38] lint test_netcdf.py --- testsuite/MDAnalysisTests/coordinates/test_netcdf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index ef1b2f9d3a6..31ade48d225 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -410,7 +410,7 @@ def test_positions(self, u): [ [-1.1455358, -2.0177484, -0.55771565], [-0.19042611, -2.2511053, -1.0282656], - [ 0.53238064, -1.5778863, -0.56737846], + [0.53238064, -1.5778863, -0.56737846], ], dtype=np.float64, ) From 0f27fc41da9278b8c70cd17bf08f76df1218fdf2 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 17 Apr 2025 11:11:00 -0400 Subject: [PATCH 20/38] small code cleanup of TRJ.py --- package/MDAnalysis/coordinates/TRJ.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 04f92e57f84..c21285ef272 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -359,7 +359,7 @@ class NCDFReader(base.ReaderBase): """Reader for `AMBER NETCDF format`_ (version 1.0). AMBER binary trajectories are automatically recognised by the - file extension ".ncdf", ".nc", and '.ncrst'. + file extension ".ncdf", ".nc", and ".ncrst". The number of atoms (`n_atoms`) does not have to be provided as it can be read from the trajectory. The trajectory reader can randomly access @@ -664,7 +664,7 @@ def _read_frame(self, frame): if self.is_restart: check_frame = () # AMBERRESTART convention files have dimensionless datasets else: - check_frame = int(frame) + check_frame = frame ts._pos[:] = self._get_var_and_scale('coordinates', check_frame) if self.has_time: @@ -691,7 +691,6 @@ def _read_frame(self, frame): # in-place ! (only lengths) self.convert_pos_from_native(ts.dimensions[:3]) - del check_frame ts.frame = frame # frame labels are 0-based self._current_frame = frame return ts From eb83b4201024ce60fe9ea943620d6f8ecbfe77a2 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 17 Apr 2025 11:43:42 -0400 Subject: [PATCH 21/38] small formatting in CHANGELOG --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index ee0a501f28d..5efb82b1199 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -34,7 +34,7 @@ Fixes directly passing them. (Issue #3520, PR #5006) Enhancements * Allow NCDF reader to read Amber Restart Files with extension `.ncrst` - (Issue #5030, PR#5031) + (Issue #5030, PR #5031) * Improve parsing of topology information from LAMMPS dump files to allow reading of mass, charge and element attributes. (Issue #3449, PR #4995) * Added timestep support for XDR writers and readers (Issue #4905, PR #4908) From d98ebabe09069947d8d390313e8c4859d09a0844 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 22 May 2025 17:58:42 -0400 Subject: [PATCH 22/38] working, failing ExceptionWarning Tests --- package/MDAnalysis/coordinates/INPCRD.py | 379 +++++++------ package/MDAnalysis/coordinates/TRJ.py | 527 ++++++++++++------ .../coordinates/test_netcdf.py | 130 ++--- testsuite/MDAnalysisTests/datafiles.py | 2 + 4 files changed, 614 insertions(+), 424 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 14f0ef1c73a..5e72a58e816 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -88,6 +88,7 @@ import logging from .timestep import Timestep +from .TRJ import NCDFMixin, NCDFPicklable from ..lib.util import store_init_arguments @@ -155,7 +156,7 @@ def parse_n_atoms(filename, **kwargs): return n_atoms -class NCRSTReader(base.SingleFrameReaderBase): +class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin): """Reader for `AMBER NETCDF format`_ (version 1.0 rev C) restart files. This reader is a :class:`SingleFrameReaderBase` adaptation of the @@ -206,7 +207,7 @@ class NCRSTReader(base.SingleFrameReaderBase): :class:`NCDFWriter` - .. versionadded: 2.5.0 + .. versionadded: 2.10.0 """ format = ['NCRST', 'NCRESTRT', 'NCRST7'] @@ -245,189 +246,199 @@ def _read_first_frame(self): """Function to read NetCDF restart file and fill timestep """ # Open netcdf file via context manager - with scipy.io.netcdf.netcdf_file(self.filename, mode='r', - mmap=self._mmap) as rstfile: - # Conventions should exist and contain the AMBERRESTART string - try: - conventions = rstfile.Conventions.decode('utf-8') - if not ('AMBERRESTART' in conventions.split(',') or - 'AMBERRESTART' in conventions.split()): - errmsg = ("NetCDF restart file {0} does not conform to " - "AMBER specifications, as detailed in " - "http://ambermd.org/netcdf/nctraj.xhtml " - "('AMBERRESTART' must be one of the tokens in " - "attribute Conventions)".format(self.filename)) - logger.fatal(errmsg) - raise TypeError(errmsg) - except AttributeError: - errmsg = ("NetCDF restart file {0} is missing a " - "Conventions value".format(self.filename)) - raise ValueError(errmsg) - - # ConventionVersion should exist and be equal to 1.0 - try: - ConventionVersion = rstfile.ConventionVersion.decode('utf-8') - if not (ConventionVersion == self.version): - wmsg = ("NCRST format is {0!s} but the reader implements " - "format {1!s}".format(ConventionVersion, - self.version)) - warnings.warn(wmsg) - logger.warning(wmsg) - except AttributeError: - errmsg = ("NCDF restart file {0} is missing a " - "ConventionVersion value".format(self.filename)) - raise ValueError(errmsg) - - # The AMBER NetCDF standard enforces 64 bit offsets - if not rstfile.version_byte == 2: - errmsg = ("NetCDF restart file {0} does not conform to AMBER " - "specifications, as detailed in " - "http://ambermd.org/netcdf/nctraj.xhtml " - "(NetCDF file does not use 64 bit offsets " - "[version_byte = 2]) ".format(self.filename)) - logger.fatal(errmsg) - raise TypeError(errmsg) - - # The specs require that dimensions->spatial == 3 exists - try: - if not rstfile.dimensions['spatial'] == 3: - errmsg = "Incorrect spatial value for NCRST file" - raise TypeError(errmsg) - except KeyError: - errmsg = ("NCDF restart file {0} does not contain spatial " - "dimension".format(self.filename)) - raise ValueError(errmsg) - - # The specs define program and programVersion as required. Here we - # just warn the users instead of raising an Error. - if not (hasattr(rstfile, 'program') and - hasattr(rstfile, 'programVersion')): - wmsg = ("This NCRST file {0} may not fully adhere to AMBER " - "standards as either the `program` or " - "`programVersion` attributes are missing".format( - self.filename)) - warnings.warn(wmsg) - logger.warning(wmsg) - - # Note: SingleFrameReaderBase class sets parsed n_atoms value to - # self.n_atom which makes for a confusing check - try: - self.n_atoms = rstfile.dimensions['atom'] - if self.n_atom is not None and self.n_atom != self.n_atoms: - raise ValueError("Supplied n_atoms ({0}) != n_atoms from " - "NetCDF restart file ({1}). " - "Note: n_atoms can be None and then the " - "restart file value is used.".format( - self.n_atom, self.n_atoms)) - except KeyError: - errmsg = ("NetCDF restart file {0} does not contain " - "atom information ".format(self.filename)) - logger.fatal(errmsg) - raise ValueError(errmsg) - - # NetCDF file title is optional - try: - self.remarks = rstfile.title - except AttributeError: - self.remarks = "" - - # Optional variables - self.has_velocities = 'velocities' in rstfile.variables - self.has_forces = 'forces' in rstfile.variables - self.periodic = 'cell_lengths' in rstfile.variables - - # Set timestep - self.ts = self._Timestep(self.n_atoms, - velocities=self.has_velocities, - forces=self.has_forces, - reader=self, - **self._ts_kwargs) - - # Check for scale_factor attributes and store them - scale_factors = {'time': 1.0, - 'cell_lengths': 1.0, - 'cell_angles': 1.0, - 'coordinates': 1.0, - 'velocities': 1.0, - 'forces': 1.0} - - for variable in rstfile.variables: - if hasattr(rstfile.variables[variable], 'scale_factor'): - if variable in scale_factors: - factor = rstfile.variables[variable].scale_factor - scale_factors[variable] = factor - else: - errmsg = ("scale_factors for variable {0} are not " - "implemented".format(variable)) - raise NotImplementedError(errmsg) - - # Note: unlike trajectories the AMBER NetCDF convention allows - # restart files to omit time when unecessary (i.e. minimizations) - try: - self._verify_units(rstfile.variables['time'].units, - 'picosecond') - self.ts.time = (rstfile.variables['time'].getValue() * - scale_factors['time']) - except KeyError: - # Warn the user and move on - wmsg = ("NCRestart file {0} does not contain time " - "information. This should be expected if the file was " - "not created from an MD trajectory (e.g. a " - "minimization)".format(self.filename)) - warnings.warn(wmsg) - logger.warning(wmsg) + # ensure maskandscale is off so we don't end up double scaling + + with NCDFPicklable(self.filename, mode='r', mmap=self._mmap, + maskandscale=False) as self.trjfile: + + self._check_conventions() + + self.n_frames = 1 + + # # Conventions should exist and contain the AMBERRESTART string + # try: + # conventions = self.trjfile.Conventions.decode('utf-8') + # if not ('AMBERRESTART' in conventions.split(',') or + # 'AMBERRESTART' in conventions.split()): + # errmsg = ("NetCDF restart file {0} does not conform to " + # "AMBER specifications, as detailed in " + # "http://ambermd.org/netcdf/nctraj.xhtml " + # "('AMBERRESTART' must be one of the tokens in " + # "attribute Conventions)".format(self.filename)) + # logger.fatal(errmsg) + # raise TypeError(errmsg) + # except AttributeError: + # errmsg = ("NetCDF restart file {0} is missing a " + # "Conventions value".format(self.filename)) + # raise ValueError(errmsg) + + # # ConventionVersion should exist and be equal to 1.0 + # try: + # ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') + # if not (ConventionVersion == self.version): + # wmsg = ("NCRST format is {0!s} but the reader implements " + # "format {1!s}".format(ConventionVersion, + # self.version)) + # warnings.warn(wmsg) + # logger.warning(wmsg) + # except AttributeError: + # errmsg = ("NCDF restart file {0} is missing a " + # "ConventionVersion value".format(self.filename)) + # raise ValueError(errmsg) + + # # The AMBER NetCDF standard enforces 64 bit offsets + # if not self.trjfile.version_byte == 2: + # errmsg = ("NetCDF restart file {0} does not conform to AMBER " + # "specifications, as detailed in " + # "http://ambermd.org/netcdf/nctraj.xhtml " + # "(NetCDF file does not use 64 bit offsets " + # "[version_byte = 2]) ".format(self.filename)) + # logger.fatal(errmsg) + # raise TypeError(errmsg) + + # # The specs require that dimensions->spatial == 3 exists + # try: + # if not self.trjfile.dimensions['spatial'] == 3: + # errmsg = "Incorrect spatial value for NCRST file" + # raise TypeError(errmsg) + # except KeyError: + # errmsg = ("NCDF restart file {0} does not contain spatial " + # "dimension".format(self.filename)) + # raise ValueError(errmsg) + + # # The specs define program and programVersion as required. Here we + # # just warn the users instead of raising an Error. + # if not (hasattr(self.trjfile, 'program') and + # hasattr(self.trjfile, 'programVersion')): + # wmsg = ("This NCRST file {0} may not fully adhere to AMBER " + # "standards as either the `program` or " + # "`programVersion` attributes are missing".format( + # self.filename)) + # warnings.warn(wmsg) + # logger.warning(wmsg) + + # # Note: SingleFrameReaderBase class sets parsed n_atoms value to + # # self.n_atom which makes for a confusing check + # try: + # self.n_atoms = self.trjfile.dimensions['atom'] + # if self.n_atom is not None and self.n_atom != self.n_atoms: + # raise ValueError("Supplied n_atoms ({0}) != n_atoms from " + # "NetCDF restart file ({1}). " + # "Note: n_atoms can be None and then the " + # "restart file value is used.".format( + # self.n_atom, self.n_atoms)) + # except KeyError: + # errmsg = ("NetCDF restart file {0} does not contain " + # "atom information ".format(self.filename)) + # logger.fatal(errmsg) + # raise ValueError(errmsg) + + # # NetCDF file title is optional + # try: + # self.remarks = self.trjfile.title + # except AttributeError: + # self.remarks = "" + + # # Optional variables + # self.has_velocities = 'velocities' in self.trjfile.variables + # self.has_forces = 'forces' in self.trjfile.variables + # self.periodic = 'cell_lengths' in self.trjfile.variables + + # # Set timestep + # self.ts = self._Timestep(self.n_atoms, + # velocities=self.has_velocities, + # forces=self.has_forces, + # reader=self, + # **self._ts_kwargs) + + # # Check for scale_factor attributes and store them + # scale_factors = {'time': 1.0, + # 'cell_lengths': 1.0, + # 'cell_angles': 1.0, + # 'coordinates': 1.0, + # 'velocities': 1.0, + # 'forces': 1.0} + + # for variable in self.trjfile.variables: + # if hasattr(self.trjfile.variables[variable], 'scale_factor'): + # if variable in self.scale_factors: + # factor = self.trjfile.variables[variable].scale_factor + # self.scale_factors[variable] = factor + # else: + # errmsg = ("scale_factors for variable {0} are not " + # "implemented".format(variable)) + # raise NotImplementedError(errmsg) + + # # Note: unlike trajectories the AMBER NetCDF convention allows + # # restart files to omit time when unecessary (i.e. minimizations) + # try: + # self._verify_units(self.trjfile.variables['time'].units, + # 'picosecond') + # self.ts.time = (self.trjfile.variables['time'].getValue() * + # scale_factors['time']) + # except KeyError: + # # Warn the user and move on + # wmsg = ("NCRestart file {0} does not contain time " + # "information. This should be expected if the file was " + # "not created from an MD trajectory (e.g. a " + # "minimization)".format(self.filename)) + # warnings.warn(wmsg) + # logger.warning(wmsg) # Single frame so we assign it to 0 self.ts.frame = 0 - # Default to length units of Angstrom - try: - self._verify_units(rstfile.variables['coordinates'].units, - 'angstrom') - self.ts._pos[:] = (rstfile.variables['coordinates'][:] * - scale_factors['coordinates']) - except KeyError: - # Technically coordinate information is not required, however - # the lack of it in a restart file is highly unlikely - errmsg = ("NetCDF restart file {0} is missing coordinate " - "information ".format(self.filename)) - logger.fatal(errmsg) - raise ValueError(errmsg) - - if self.has_velocities: - self._verify_units(rstfile.variables['velocities'].units, - 'angstrom/picosecond') - self.ts._velocities[:] = (rstfile.variables['velocities'][:] * - scale_factors['velocities']) - - # The presence of forces in an ncrst is rare but possible - if self.has_forces: - self._verify_units(rstfile.variables['forces'].units, - 'kilocalorie/mole/angstrom') - self.ts._forces[:] = (rstfile.variables['forces'][:] * - scale_factors['forces']) - - # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] - # Unlike the NCDFReader, `degrees` is not accepted - if self.periodic: - self._verify_units(rstfile.variables['cell_lengths'].units, - 'angstrom') - self._verify_units(rstfile.variables['cell_angles'].units, - 'degree') - self.ts._unitcell[:3] = (rstfile.variables['cell_lengths'][:] * - scale_factors['cell_lengths']) - self.ts._unitcell[3:] = (rstfile.variables['cell_angles'][:] * - scale_factors['cell_angles']) - - # Convert units inplace - if self.convert_units: - self.convert_pos_from_native(self.ts._pos) - self.convert_time_from_native(self.ts.time) - if self.has_velocities: - self.convert_velocities_from_native(self.ts._velocities, - inplace=True) - if self.has_forces: - self.convert_forces_from_native(self.ts._forces, - inplace=True) - if self.periodic: - self.convert_pos_from_native(self.ts._unitcell[:3]) + # # Default to length units of Angstrom + # try: + # self._verify_units(self.trjfile.variables['coordinates'].units, + # 'angstrom') + # self.ts._pos[:] = (self.trjfile.variables['coordinates'][:] * + # scale_factors['coordinates']) + # except KeyError: + # # Technically coordinate information is not required, however + # # the lack of it in a restart file is highly unlikely + # errmsg = ("NetCDF restart file {0} is missing coordinate " + # "information ".format(self.filename)) + # logger.fatal(errmsg) + # raise ValueError(errmsg) + + + self._read_values(frame=()) # AMBERRESTART convention files have dimensionless datasets + + # if self.has_velocities: + # self._verify_units(self.trjfile.variables['velocities'].units, + # 'angstrom/picosecond') + # self.ts._velocities[:] = (self.trjfile.variables['velocities'][:] * + # scale_factors['velocities']) + + # # The presence of forces in an ncrst is rare but possible + # if self.has_forces: + # self._verify_units(self.trjfile.variables['forces'].units, + # 'kilocalorie/mole/angstrom') + # self.ts._forces[:] = (self.trjfile.variables['forces'][:] * + # scale_factors['forces']) + + # # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] + # # Unlike the NCDFReader, `degrees` is not accepted + # if self.periodic: + # self._verify_units(self.trjfile.variables['cell_lengths'].units, + # 'angstrom') + # self._verify_units(self.trjfile.variables['cell_angles'].units, + # 'degree') + # self.ts._unitcell[:3] = (self.trjfile.variables['cell_lengths'][:] * + # scale_factors['cell_lengths']) + # self.ts._unitcell[3:] = (self.trjfile.variables['cell_angles'][:] * + # scale_factors['cell_angles']) + + # # Convert units inplace + # if self.convert_units: + # self.convert_pos_from_native(self.ts._pos) + # self.convert_time_from_native(self.ts.time) + # if self.has_velocities: + # self.convert_velocities_from_native(self.ts._velocities, + # inplace=True) + # if self.has_forces: + # self.convert_forces_from_native(self.ts._forces, + # inplace=True) + # if self.periodic: + # self.convert_pos_from_native(self.ts._unitcell[:3]) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index c21285ef272..344dd2971de 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -355,99 +355,10 @@ def close(self): self.trjfile = None -class NCDFReader(base.ReaderBase): - """Reader for `AMBER NETCDF format`_ (version 1.0). - - AMBER binary trajectories are automatically recognised by the - file extension ".ncdf", ".nc", and ".ncrst". - - The number of atoms (`n_atoms`) does not have to be provided as it can - be read from the trajectory. The trajectory reader can randomly access - frames and therefore supports direct indexing (with 0-based frame - indices) and full-feature trajectory iteration, including slicing. - - Velocities are autodetected and read into the - :attr:`Timestep._velocities` attribute. - - Forces are autodetected and read into the - :attr:`Timestep._forces` attribute. - - Periodic unit cell information is detected and used to populate the - :attr:`Timestep.dimensions` attribute. (If no unit cell is available in - the trajectory, then :attr:`Timestep.dimensions` will return - ``[0,0,0,0,0,0]``). - - Current limitations: - - * only trajectories with time in ps and lengths in Angstroem are processed - - The NCDF reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` must - be installed. It supports the *mmap* keyword argument (when reading): - ``mmap=True`` is memory efficient and directly maps the trajectory on disk - to memory (using the :class:`~mmap.mmap`); ``mmap=False`` may consume large - amounts of memory because it loads the whole trajectory into memory but it - might be faster. The default is ``mmap=None`` and then default behavior of - :class:`scipy.io.netcdf_file` prevails, i.e. ``True`` when - *filename* is a file name, ``False`` when *filename* is a file-like object. - - .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml - - See Also - -------- - :class:`NCDFWriter` - - - .. versionadded: 0.7.6 - .. versionchanged:: 0.10.0 - Added ability to read Forces - .. versionchanged:: 0.11.0 - Frame labels now 0-based instead of 1-based. - kwarg `delta` renamed to `dt`, for uniformity with other Readers. - .. versionchanged:: 0.17.0 - Uses :mod:`scipy.io.netcdf` and supports the *mmap* kwarg. - .. versionchanged:: 0.20.0 - Now reads scale_factors for all expected AMBER convention variables. - Timestep variables now adhere standard MDAnalysis units, with lengths - of angstrom, time of ps, velocity of angstrom/ps and force of - kJ/(mol*Angstrom). It is noted that with 0.19.2 and earlier versions, - velocities would have often been reported in values of angstrom/AKMA - time units instead (Issue #2323). - .. versionchanged:: 1.0.0 - Support for reading `degrees` units for `cell_angles` has now been - removed (Issue #2327) - .. versionchanged:: 2.0.0 - Now use a picklable :class:`scipy.io.netcdf_file`-- - :class:`NCDFPicklable`. - Reading of `dt` now defaults to 1.0 ps if `dt` cannot be extracted from - the first two frames of the trajectory. - :meth:`Writer` now also sets `convert_units`, `velocities`, `forces` and - `scale_factor` information for the :class:`NCDFWriter`. - .. versionchanged:: 2.10.0 - Now reads `AMBERRESTART` convention `.ncrst` files. - - """ - - format = ['NCDF', 'NC', 'NCRST'] - multiframe = True - version = "1.0" - units = {'time': 'ps', - 'length': 'Angstrom', - 'velocity': 'Angstrom/ps', - 'force': 'kcal/(mol*Angstrom)'} - - _Timestep = Timestep - - @store_init_arguments - def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): - - self._mmap = mmap - - super(NCDFReader, self).__init__(filename, **kwargs) - - # ensure maskandscale is off so we don't end up double scaling - self.trjfile = NCDFPicklable(self.filename, - mmap=self._mmap, - maskandscale=False) +class NCDFMixin(): + def _check_conventions(self, n_atoms=None): + convention = 'AMBERRESTART' if self.__class__.__name__ == 'NCRSTReader' else 'AMBER' + file_format = 'restart file' if self.__class__.__name__ == 'NCRSTReader' else 'trajectory' # AMBER NetCDF files should always have a convention try: @@ -455,21 +366,17 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): check = [conventions.decode('utf-8').split(','), conventions.decode('utf-8').split()] - if 'AMBER' in check[0] or 'AMBER' in check[1]: - self.is_restart = False - elif 'AMBERRESTART' in check[0] or 'AMBERRESTART' in check[1]: - self.is_restart = True - else: - errmsg = ("NCDF trajectory {0} does not conform to AMBER " + if not (convention in check[0] or convention in check[1]): + errmsg = ("NCDF {0} {1} does not conform to AMBER " "specifications, " "http://ambermd.org/netcdf/nctraj.xhtml " - "('AMBER' must be one of the token in attribute " - "Conventions)".format(self.filename)) + "({2} must be one of the token in attribute " + "Conventions)".format(file_format, self.filename, convention)) logger.fatal(errmsg) raise TypeError(errmsg) except AttributeError: - errmsg = "NCDF trajectory {0} is missing Conventions".format( - self.filename) + errmsg = "NCDF {0} {1} is missing Conventions".format( + file_format, self.filename) logger.fatal(errmsg) raise ValueError(errmsg) from None @@ -477,23 +384,23 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): try: ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') if not ConventionVersion == self.version: - wmsg = ("NCDF trajectory format is {0!s} but the reader " + wmsg = ("NCDF file format is {0!s} but the reader " "implements format {1!s}".format( ConventionVersion, self.version)) warnings.warn(wmsg) logger.warning(wmsg) except AttributeError: - errmsg = "NCDF trajectory {0} is missing ConventionVersion".format( - self.filename) + errmsg = "NCDF {0} {1} is missing ConventionVersion".format( + file_format, self.filename) raise ValueError(errmsg) from None # The AMBER NetCDF standard enforces 64 bit offsets if not self.trjfile.version_byte == 2: - errmsg = ("NCDF trajectory {0} does not conform to AMBER " + errmsg = ("NCDF {0} {1} does not conform to AMBER " "specifications, as detailed in " "https://ambermd.org/netcdf/nctraj.xhtml " "(NetCDF file does not use 64 bit offsets " - "[version_byte = 2])".format(self.filename)) + "[version_byte = 2])".format(file_format, self.filename)) logger.fatal(errmsg) raise TypeError(errmsg) @@ -503,16 +410,16 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): errmsg = "Incorrect spatial value for NCDF trajectory file" raise TypeError(errmsg) except KeyError: - errmsg = "NCDF trajectory does not contain spatial dimension" + errmsg = "NCDF {0} does not contain spatial dimension".format(file_format) raise ValueError(errmsg) from None # AMBER NetCDF specs require program and programVersion. Warn users # if those attributes do not exist if not (hasattr(self.trjfile, 'program') and hasattr(self.trjfile, 'programVersion')): - wmsg = ("NCDF trajectory {0} may not fully adhere to AMBER " + wmsg = ("NCDF {0} {1} may not fully adhere to AMBER " "standards as either the `program` or `programVersion` " - "attributes are missing".format(self.filename)) + "attributes are missing".format(file_format, self.filename)) warnings.warn(wmsg) logger.warning(wmsg) @@ -524,26 +431,26 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): "is used!".format(n_atoms, self.n_atoms)) raise ValueError(errmsg) except KeyError: - errmsg = ("NCDF trajectory {0} does not contain atom " - "information".format(self.filename)) + errmsg = ("NCDF {0} {1} does not contain atom " + "information".format(file_format, self.filename)) raise ValueError(errmsg) from None - try: - self.n_frames = self.trjfile.dimensions['frame'] - # example trajectory when read with scipy.io.netcdf has - # dimensions['frame'] == None (indicating a record dimension that - # can grow) whereas if read with netCDF4 I get - # len(dimensions['frame']) == 10: in any case, we need to get - # the number of frames from somewhere such as the time variable: - if self.n_frames is None: - self.n_frames = self.trjfile.variables['coordinates'].shape[0] - except KeyError: - if self.is_restart: - self.n_frames = 1 - else: - errmsg = (f"NCDF trajectory {self.filename} does not contain " - f"frame information") - raise ValueError(errmsg) from None + # try: + # self.n_frames = self.trjfile.dimensions['frame'] + # # example trajectory when read with scipy.io.netcdf has + # # dimensions['frame'] == None (indicating a record dimension that + # # can grow) whereas if read with netCDF4 I get + # # len(dimensions['frame']) == 10: in any case, we need to get + # # the number of frames from somewhere such as the time variable: + # if self.n_frames is None: + # self.n_frames = self.trjfile.variables['coordinates'].shape[0] + # except KeyError: + # if self.is_restart: + # self.n_frames = 1 + # else: + # errmsg = ("NCDF {file_format} {self.filename} does not contain " + # "frame information").format + # raise ValueError(errmsg) from None try: self.remarks = self.trjfile.title @@ -616,8 +523,44 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): reader=self, # for dt **self._ts_kwargs) - # load first data frame - self._read_frame(0) + + def _read_values(self, frame): + ts = self.ts + + if self.trjfile is None: + raise IOError("Trajectory is closed") + if (not isinstance(frame, tuple)) and (np.dtype(type(frame)) != np.dtype(int)): + # convention... for netcdf could also be a slice + raise TypeError("frame must be a positive integer or zero") + if (not isinstance(frame, tuple)) and (frame >= self.n_frames or frame < 0): + raise IndexError("frame index must be 0 <= frame < {0}".format( + self.n_frames)) + # note: self.trjfile.variables['coordinates'].shape == (frames, n_atoms, 3) + + ts._pos[:] = self._get_var_and_scale('coordinates', frame) + if self.has_time: + ts.time = self._get_var_and_scale('time', frame) + if self.has_velocities: + ts._velocities[:] = self._get_var_and_scale('velocities', frame) + if self.has_forces: + ts._forces[:] = self._get_var_and_scale('forces', frame) + if self.periodic: + unitcell = np.zeros(6) + unitcell[:3] = self._get_var_and_scale('cell_lengths', frame) + unitcell[3:] = self._get_var_and_scale('cell_angles', frame) + ts.dimensions = unitcell + if self.convert_units: + self.convert_pos_from_native(ts._pos) # in-place ! + self.convert_time_from_native(ts.time) # in-place ! + if self.has_velocities: + self.convert_velocities_from_native(ts._velocities, + inplace=True) + if self.has_forces: + self.convert_forces_from_native(ts._forces, inplace=True) + if self.periodic: + # in-place ! (only lengths) + self.convert_pos_from_native(ts.dimensions[:3]) + @staticmethod def _verify_units(eval_unit, expected_units): @@ -627,11 +570,6 @@ def _verify_units(eval_unit, expected_units): eval_unit.decode('utf-8'), expected_units)) raise NotImplementedError(errmsg) - @staticmethod - def parse_n_atoms(filename, **kwargs): - with scipy.io.netcdf_file(filename, mmap=None) as f: - n_atoms = f.dimensions['atom'] - return n_atoms def _get_var_and_scale(self, variable, frame): """Helper function to get variable at given frame from NETCDF file and @@ -648,48 +586,287 @@ def _get_var_and_scale(self, variable, frame): else: return self.trjfile.variables[variable][frame] * scale_factor - def _read_frame(self, frame): - ts = self.ts - if self.trjfile is None: - raise IOError("Trajectory is closed") - if np.dtype(type(frame)) != np.dtype(int): - # convention... for netcdf could also be a slice - raise TypeError("frame must be a positive integer or zero") - if (frame >= self.n_frames or frame < 0): - raise IndexError("frame index must be 0 <= frame < {0}".format( - self.n_frames)) - # note: self.trjfile.variables['coordinates'].shape == (frames, n_atoms, 3) - if self.is_restart: - check_frame = () # AMBERRESTART convention files have dimensionless datasets - else: - check_frame = frame +class NCDFReader(base.ReaderBase, NCDFMixin): + """Reader for `AMBER NETCDF format`_ (version 1.0). - ts._pos[:] = self._get_var_and_scale('coordinates', check_frame) - if self.has_time: - ts.time = self._get_var_and_scale('time', check_frame) - if self.has_velocities: - ts._velocities[:] = self._get_var_and_scale('velocities', check_frame) - if self.has_forces: - ts._forces[:] = self._get_var_and_scale('forces', check_frame) - if self.periodic: - unitcell = np.zeros(6) - unitcell[:3] = self._get_var_and_scale('cell_lengths', check_frame) - unitcell[3:] = self._get_var_and_scale('cell_angles', check_frame) - ts.dimensions = unitcell - if self.convert_units: - self.convert_pos_from_native(ts._pos) # in-place ! - self.convert_time_from_native( - ts.time) # in-place ! (hope this works...) - if self.has_velocities: - self.convert_velocities_from_native(ts._velocities, - inplace=True) - if self.has_forces: - self.convert_forces_from_native(ts._forces, inplace=True) - if self.periodic: - # in-place ! (only lengths) - self.convert_pos_from_native(ts.dimensions[:3]) + AMBER binary trajectories are automatically recognised by the + file extension ".ncdf". + + The number of atoms (`n_atoms`) does not have to be provided as it can + be read from the trajectory. The trajectory reader can randomly access + frames and therefore supports direct indexing (with 0-based frame + indices) and full-feature trajectory iteration, including slicing. + + Velocities are autodetected and read into the + :attr:`Timestep._velocities` attribute. + + Forces are autodetected and read into the + :attr:`Timestep._forces` attribute. + + Periodic unit cell information is detected and used to populate the + :attr:`Timestep.dimensions` attribute. (If no unit cell is available in + the trajectory, then :attr:`Timestep.dimensions` will return + ``[0,0,0,0,0,0]``). + + Current limitations: + + * only trajectories with time in ps and lengths in Angstroem are processed + + The NCDF reader uses :mod:`scipy.io.netcdf` and therefore :mod:`scipy` must + be installed. It supports the *mmap* keyword argument (when reading): + ``mmap=True`` is memory efficient and directly maps the trajectory on disk + to memory (using the :class:`~mmap.mmap`); ``mmap=False`` may consume large + amounts of memory because it loads the whole trajectory into memory but it + might be faster. The default is ``mmap=None`` and then default behavior of + :class:`scipy.io.netcdf_file` prevails, i.e. ``True`` when + *filename* is a file name, ``False`` when *filename* is a file-like object. + + .. _AMBER NETCDF format: http://ambermd.org/netcdf/nctraj.xhtml + + See Also + -------- + :class:`NCDFWriter` + + + .. versionadded: 0.7.6 + .. versionchanged:: 0.10.0 + Added ability to read Forces + .. versionchanged:: 0.11.0 + Frame labels now 0-based instead of 1-based. + kwarg `delta` renamed to `dt`, for uniformity with other Readers. + .. versionchanged:: 0.17.0 + Uses :mod:`scipy.io.netcdf` and supports the *mmap* kwarg. + .. versionchanged:: 0.20.0 + Now reads scale_factors for all expected AMBER convention variables. + Timestep variables now adhere standard MDAnalysis units, with lengths + of angstrom, time of ps, velocity of angstrom/ps and force of + kJ/(mol*Angstrom). It is noted that with 0.19.2 and earlier versions, + velocities would have often been reported in values of angstrom/AKMA + time units instead (Issue #2323). + .. versionchanged:: 1.0.0 + Support for reading `degrees` units for `cell_angles` has now been + removed (Issue #2327) + .. versionchanged:: 2.0.0 + Now use a picklable :class:`scipy.io.netcdf_file`-- + :class:`NCDFPicklable`. + Reading of `dt` now defaults to 1.0 ps if `dt` cannot be extracted from + the first two frames of the trajectory. + :meth:`Writer` now also sets `convert_units`, `velocities`, `forces` and + `scale_factor` information for the :class:`NCDFWriter`. + + """ + + format = ['NCDF', 'NC'] + multiframe = True + version = "1.0" + units = {'time': 'ps', + 'length': 'Angstrom', + 'velocity': 'Angstrom/ps', + 'force': 'kcal/(mol*Angstrom)'} + + _Timestep = Timestep + + @store_init_arguments + def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): + + self._mmap = mmap + + super(NCDFReader, self).__init__(filename, **kwargs) + + # ensure maskandscale is off so we don't end up double scaling + self.trjfile = NCDFPicklable(self.filename, + mmap=self._mmap, + maskandscale=False) + + self._check_conventions(n_atoms) + + try: + self.n_frames = self.trjfile.dimensions['frame'] + # example trajectory when read with scipy.io.netcdf has + # dimensions['frame'] == None (indicating a record dimension that + # can grow) whereas if read with netCDF4 I get + # len(dimensions['frame']) == 10: in any case, we need to get + # the number of frames from somewhere such as the time variable: + if self.n_frames is None: + self.n_frames = self.trjfile.variables['coordinates'].shape[0] + except KeyError: + errmsg = (f"NCDF trajectory {self.filename} does not contain " + f"frame information") + raise ValueError(errmsg) from None + + # # AMBER NetCDF files should always have a convention + # try: + # conventions = self.trjfile.Conventions + # if not ('AMBER' in conventions.decode('utf-8').split(',') or + # 'AMBER' in conventions.decode('utf-8').split()): + # errmsg = ("NCDF trajectory {0} does not conform to AMBER " + # "specifications, " + # "http://ambermd.org/netcdf/nctraj.xhtml " + # "('AMBER' must be one of the token in attribute " + # "Conventions)".format(self.filename)) + # logger.fatal(errmsg) + # raise TypeError(errmsg) + # except AttributeError: + # errmsg = "NCDF trajectory {0} is missing Conventions".format( + # self.filename) + # logger.fatal(errmsg) + # raise ValueError(errmsg) from None + + # # AMBER NetCDF files should also have a ConventionVersion + # try: + # ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') + # if not ConventionVersion == self.version: + # wmsg = ("NCDF trajectory format is {0!s} but the reader " + # "implements format {1!s}".format( + # ConventionVersion, self.version)) + # warnings.warn(wmsg) + # logger.warning(wmsg) + # except AttributeError: + # errmsg = "NCDF trajectory {0} is missing ConventionVersion".format( + # self.filename) + # raise ValueError(errmsg) from None + + # # The AMBER NetCDF standard enforces 64 bit offsets + # if not self.trjfile.version_byte == 2: + # errmsg = ("NCDF trajectory {0} does not conform to AMBER " + # "specifications, as detailed in " + # "https://ambermd.org/netcdf/nctraj.xhtml " + # "(NetCDF file does not use 64 bit offsets " + # "[version_byte = 2])".format(self.filename)) + # logger.fatal(errmsg) + # raise TypeError(errmsg) + + # # The AMBER NetCDF standard enforces 3D coordinates + # try: + # if not self.trjfile.dimensions['spatial'] == 3: + # errmsg = "Incorrect spatial value for NCDF trajectory file" + # raise TypeError(errmsg) + # except KeyError: + # errmsg = "NCDF trajectory does not contain spatial dimension" + # raise ValueError(errmsg) from None + + # # AMBER NetCDF specs require program and programVersion. Warn users + # # if those attributes do not exist + # if not (hasattr(self.trjfile, 'program') and + # hasattr(self.trjfile, 'programVersion')): + # wmsg = ("NCDF trajectory {0} may not fully adhere to AMBER " + # "standards as either the `program` or `programVersion` " + # "attributes are missing".format(self.filename)) + # warnings.warn(wmsg) + # logger.warning(wmsg) + + # try: + # self.n_atoms = self.trjfile.dimensions['atom'] + # if n_atoms is not None and n_atoms != self.n_atoms: + # errmsg = ("Supplied n_atoms ({0}) != natom from ncdf ({1}). " + # "Note: n_atoms can be None and then the ncdf value " + # "is used!".format(n_atoms, self.n_atoms)) + # raise ValueError(errmsg) + # except KeyError: + # errmsg = ("NCDF trajectory {0} does not contain atom " + # "information".format(self.filename)) + # raise ValueError(errmsg) from None + + # try: + # self.n_frames = self.trjfile.dimensions['frame'] + # # example trajectory when read with scipy.io.netcdf has + # # dimensions['frame'] == None (indicating a record dimension that + # # can grow) whereas if read with netCDF4 I get + # # len(dimensions['frame']) == 10: in any case, we need to get + # # the number of frames from somewhere such as the time variable: + # if self.n_frames is None: + # self.n_frames = self.trjfile.variables['coordinates'].shape[0] + # except KeyError: + # errmsg = (f"NCDF trajectory {self.filename} does not contain " + # f"frame information") + # raise ValueError(errmsg) from None + + # try: + # self.remarks = self.trjfile.title + # except AttributeError: + # self.remarks = "" + # # other metadata (*= requd): + # # - application AMBER + # # + + # # checks for not-implemented features (other units would need to be + # # hacked into MDAnalysis.units) + # try: + # self._verify_units(self.trjfile.variables['time'].units, 'picosecond') + # self.has_time = True + # except KeyError: + # self.has_time = False + # wmsg = ("NCDF trajectory does not contain `time` information;" + # " `time` will be set as an increasing index") + # warnings.warn(wmsg) + # logger.warning(wmsg) + + + # self._verify_units(self.trjfile.variables['coordinates'].units, + # 'angstrom') + + # # Check for scale_factor attributes for all data variables and + # # store this to multiply through later (Issue #2323) + # self.scale_factors = {'time': None, + # 'cell_lengths': None, + # 'cell_angles': None, + # 'coordinates': None, + # 'velocities': None, + # 'forces': None} + + # for variable in self.trjfile.variables: + # if hasattr(self.trjfile.variables[variable], 'scale_factor'): + # if variable in self.scale_factors: + # scale_factor = self.trjfile.variables[variable].scale_factor + # if not isinstance(scale_factor, (float, np.floating)): + # raise TypeError(f"{scale_factor} is not a float") + # self.scale_factors[variable] = scale_factor + # else: + # errmsg = ("scale_factors for variable {0} are " + # "not implemented".format(variable)) + # raise NotImplementedError(errmsg) + + # self.has_velocities = 'velocities' in self.trjfile.variables + # if self.has_velocities: + # self._verify_units(self.trjfile.variables['velocities'].units, + # 'angstrom/picosecond') + + # self.has_forces = 'forces' in self.trjfile.variables + # if self.has_forces: + # self._verify_units(self.trjfile.variables['forces'].units, + # 'kilocalorie/mole/angstrom') + + # self.periodic = 'cell_lengths' in self.trjfile.variables + # if self.periodic: + # self._verify_units(self.trjfile.variables['cell_lengths'].units, + # 'angstrom') + # # As of v1.0.0 only `degree` is accepted as a unit + # cell_angle_units = self.trjfile.variables['cell_angles'].units + # self._verify_units(cell_angle_units, 'degree') + + # self._current_frame = 0 + + # self.ts = self._Timestep(self.n_atoms, + # velocities=self.has_velocities, + # forces=self.has_forces, + # reader=self, # for dt + # **self._ts_kwargs) + + # load first data frame + self._read_frame(0) + + @staticmethod + def parse_n_atoms(filename, **kwargs): + with scipy.io.netcdf_file(filename, mmap=None) as f: + n_atoms = f.dimensions['atom'] + return n_atoms + + def _read_frame(self, frame): + ts = self.ts + + self._read_values(frame) ts.frame = frame # frame labels are 0-based self._current_frame = frame diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index 31ade48d225..a3085a80564 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -391,70 +391,70 @@ def test_warn_user_no_time_information(self, u): u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) -class TestNCDFReader5(object): - """NCRST Restart File with positions and forces, exported by CPPTRAJ. - - Contributed by Jeremy M. G. Leung - """ - - prec = 6 - - @pytest.fixture(scope="class") - def u(self): - return mda.Universe(PRMNCRST, TRJNCRST) - - def test_positions(self, u): - """Check positions on first frame""" - u.trajectory[0] - ref_1 = np.array( - [ - [-1.1455358, -2.0177484, -0.55771565], - [-0.19042611, -2.2511053, -1.0282656], - [0.53238064, -1.5778863, -0.56737846], - ], - dtype=np.float64, - ) - assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec) - - def test_velocities(self, u): - """Check forces on first frame""" - u.trajectory[0] - ref_1 = np.array( - [ - [11.86471367, 31.22108269, -4.03538418], - [7.36676359, -4.68035316, 1.78124952], - [12.86675262, 1.39324546, -14.97190762], - ], - dtype=np.float64, - ) - assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec) - - def test_forces(self, u): - """Check forces on first frame""" - u.trajectory[0] - ref_1 = np.array( - [ - [-9.7262249, -0.37627634, -24.79876137], - [-32.43384552, 37.47783279, -12.45422745], - [24.10939026, -19.80618095, -17.09523582], - ], - dtype=np.float64, - ) - assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec) - - def test_time(self, u): - """Check time on first frame""" - ref = 5.0 - assert_almost_equal(ref, u.trajectory[0].time, self.prec) - - def test_dt(self, u): - """Default 1.0 fs""" - ref = 1.0 - assert_almost_equal(ref, u.trajectory.dt, self.prec) - assert_almost_equal(ref, u.trajectory.ts.dt, self.prec) - - def test_box(self, u): - assert u.trajectory[0].dimensions is None +#class TestNCDFReader5(object): +# """NCRST Restart File with positions and forces, exported by CPPTRAJ. +# +# Contributed by Jeremy M. G. Leung +# """ +# +# prec = 6 +# +# @pytest.fixture(scope="class") +# def u(self): +# return mda.Universe(PRMNCRST, TRJNCRST) +# +# def test_positions(self, u): +# """Check positions on first frame""" +# u.trajectory[0] +# ref_1 = np.array( +# [ +# [-1.1455358, -2.0177484, -0.55771565], +# [-0.19042611, -2.2511053, -1.0282656], +# [0.53238064, -1.5778863, -0.56737846], +# ], +# dtype=np.float64, +# ) +# assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec) +# +# def test_velocities(self, u): +# """Check forces on first frame""" +# u.trajectory[0] +# ref_1 = np.array( +# [ +# [11.86471367, 31.22108269, -4.03538418], +# [7.36676359, -4.68035316, 1.78124952], +# [12.86675262, 1.39324546, -14.97190762], +# ], +# dtype=np.float64, +# ) +# assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec) +# +# def test_forces(self, u): +# """Check forces on first frame""" +# u.trajectory[0] +# ref_1 = np.array( +# [ +# [-9.7262249, -0.37627634, -24.79876137], +# [-32.43384552, 37.47783279, -12.45422745], +# [24.10939026, -19.80618095, -17.09523582], +# ], +# dtype=np.float64, +# ) +# assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec) +# +# def test_time(self, u): +# """Check time on first frame""" +# ref = 5.0 +# assert_almost_equal(ref, u.trajectory[0].time, self.prec) +# +# def test_dt(self, u): +# """Default 1.0 fs""" +# ref = 1.0 +# assert_almost_equal(ref, u.trajectory.dt, self.prec) +# assert_almost_equal(ref, u.trajectory.ts.dt, self.prec) +# +# def test_box(self, u): +# assert u.trajectory[0].dimensions is None class _NCDFGenerator(object): @@ -778,7 +778,7 @@ def test_conventionversion_warn(self, tmpdir): assert len(record) == 1 wmsg = ( - "NCDF trajectory format is 2.0 but the reader " + "NCDF file format is 2.0 but the reader " "implements format 1.0" ) assert str(record[0].message.args[0]) == wmsg diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 51f5116d55e..8b4a6b70bd8 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -193,6 +193,8 @@ "PRMcs", # Amber (format, Issue 1331) "PRMNCRST", # Amber topology for ncrst with positions/forces/velocities "TRJNCRST", # Amber ncrst with positions/forces/velocties + "PRMNCRSTbox", + "NCRSTbox", "PRM_NCBOX", "TRJ_NCBOX", # Amber parm7 + nc w/ pos/forces/vels/box "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) From 37b7e1e30cbc144579ed57409323a764a783ac2e Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 22 May 2025 18:19:40 -0400 Subject: [PATCH 23/38] cleanup --- package/MDAnalysis/coordinates/INPCRD.py | 184 +---------------------- 1 file changed, 1 insertion(+), 183 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 5e72a58e816..b207ed8bdc6 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -253,192 +253,10 @@ def _read_first_frame(self): self._check_conventions() - self.n_frames = 1 - - # # Conventions should exist and contain the AMBERRESTART string - # try: - # conventions = self.trjfile.Conventions.decode('utf-8') - # if not ('AMBERRESTART' in conventions.split(',') or - # 'AMBERRESTART' in conventions.split()): - # errmsg = ("NetCDF restart file {0} does not conform to " - # "AMBER specifications, as detailed in " - # "http://ambermd.org/netcdf/nctraj.xhtml " - # "('AMBERRESTART' must be one of the tokens in " - # "attribute Conventions)".format(self.filename)) - # logger.fatal(errmsg) - # raise TypeError(errmsg) - # except AttributeError: - # errmsg = ("NetCDF restart file {0} is missing a " - # "Conventions value".format(self.filename)) - # raise ValueError(errmsg) - - # # ConventionVersion should exist and be equal to 1.0 - # try: - # ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') - # if not (ConventionVersion == self.version): - # wmsg = ("NCRST format is {0!s} but the reader implements " - # "format {1!s}".format(ConventionVersion, - # self.version)) - # warnings.warn(wmsg) - # logger.warning(wmsg) - # except AttributeError: - # errmsg = ("NCDF restart file {0} is missing a " - # "ConventionVersion value".format(self.filename)) - # raise ValueError(errmsg) - - # # The AMBER NetCDF standard enforces 64 bit offsets - # if not self.trjfile.version_byte == 2: - # errmsg = ("NetCDF restart file {0} does not conform to AMBER " - # "specifications, as detailed in " - # "http://ambermd.org/netcdf/nctraj.xhtml " - # "(NetCDF file does not use 64 bit offsets " - # "[version_byte = 2]) ".format(self.filename)) - # logger.fatal(errmsg) - # raise TypeError(errmsg) - - # # The specs require that dimensions->spatial == 3 exists - # try: - # if not self.trjfile.dimensions['spatial'] == 3: - # errmsg = "Incorrect spatial value for NCRST file" - # raise TypeError(errmsg) - # except KeyError: - # errmsg = ("NCDF restart file {0} does not contain spatial " - # "dimension".format(self.filename)) - # raise ValueError(errmsg) - - # # The specs define program and programVersion as required. Here we - # # just warn the users instead of raising an Error. - # if not (hasattr(self.trjfile, 'program') and - # hasattr(self.trjfile, 'programVersion')): - # wmsg = ("This NCRST file {0} may not fully adhere to AMBER " - # "standards as either the `program` or " - # "`programVersion` attributes are missing".format( - # self.filename)) - # warnings.warn(wmsg) - # logger.warning(wmsg) - - # # Note: SingleFrameReaderBase class sets parsed n_atoms value to - # # self.n_atom which makes for a confusing check - # try: - # self.n_atoms = self.trjfile.dimensions['atom'] - # if self.n_atom is not None and self.n_atom != self.n_atoms: - # raise ValueError("Supplied n_atoms ({0}) != n_atoms from " - # "NetCDF restart file ({1}). " - # "Note: n_atoms can be None and then the " - # "restart file value is used.".format( - # self.n_atom, self.n_atoms)) - # except KeyError: - # errmsg = ("NetCDF restart file {0} does not contain " - # "atom information ".format(self.filename)) - # logger.fatal(errmsg) - # raise ValueError(errmsg) - - # # NetCDF file title is optional - # try: - # self.remarks = self.trjfile.title - # except AttributeError: - # self.remarks = "" - - # # Optional variables - # self.has_velocities = 'velocities' in self.trjfile.variables - # self.has_forces = 'forces' in self.trjfile.variables - # self.periodic = 'cell_lengths' in self.trjfile.variables - - # # Set timestep - # self.ts = self._Timestep(self.n_atoms, - # velocities=self.has_velocities, - # forces=self.has_forces, - # reader=self, - # **self._ts_kwargs) - - # # Check for scale_factor attributes and store them - # scale_factors = {'time': 1.0, - # 'cell_lengths': 1.0, - # 'cell_angles': 1.0, - # 'coordinates': 1.0, - # 'velocities': 1.0, - # 'forces': 1.0} - - # for variable in self.trjfile.variables: - # if hasattr(self.trjfile.variables[variable], 'scale_factor'): - # if variable in self.scale_factors: - # factor = self.trjfile.variables[variable].scale_factor - # self.scale_factors[variable] = factor - # else: - # errmsg = ("scale_factors for variable {0} are not " - # "implemented".format(variable)) - # raise NotImplementedError(errmsg) - - # # Note: unlike trajectories the AMBER NetCDF convention allows - # # restart files to omit time when unecessary (i.e. minimizations) - # try: - # self._verify_units(self.trjfile.variables['time'].units, - # 'picosecond') - # self.ts.time = (self.trjfile.variables['time'].getValue() * - # scale_factors['time']) - # except KeyError: - # # Warn the user and move on - # wmsg = ("NCRestart file {0} does not contain time " - # "information. This should be expected if the file was " - # "not created from an MD trajectory (e.g. a " - # "minimization)".format(self.filename)) - # warnings.warn(wmsg) - # logger.warning(wmsg) + self.n_frames = 0 # Single frame so we assign it to 0 self.ts.frame = 0 - # # Default to length units of Angstrom - # try: - # self._verify_units(self.trjfile.variables['coordinates'].units, - # 'angstrom') - # self.ts._pos[:] = (self.trjfile.variables['coordinates'][:] * - # scale_factors['coordinates']) - # except KeyError: - # # Technically coordinate information is not required, however - # # the lack of it in a restart file is highly unlikely - # errmsg = ("NetCDF restart file {0} is missing coordinate " - # "information ".format(self.filename)) - # logger.fatal(errmsg) - # raise ValueError(errmsg) - - self._read_values(frame=()) # AMBERRESTART convention files have dimensionless datasets - # if self.has_velocities: - # self._verify_units(self.trjfile.variables['velocities'].units, - # 'angstrom/picosecond') - # self.ts._velocities[:] = (self.trjfile.variables['velocities'][:] * - # scale_factors['velocities']) - - # # The presence of forces in an ncrst is rare but possible - # if self.has_forces: - # self._verify_units(self.trjfile.variables['forces'].units, - # 'kilocalorie/mole/angstrom') - # self.ts._forces[:] = (self.trjfile.variables['forces'][:] * - # scale_factors['forces']) - - # # If false u.dimensions is set to [0., 0., 0., 0., 0., 0] - # # Unlike the NCDFReader, `degrees` is not accepted - # if self.periodic: - # self._verify_units(self.trjfile.variables['cell_lengths'].units, - # 'angstrom') - # self._verify_units(self.trjfile.variables['cell_angles'].units, - # 'degree') - # self.ts._unitcell[:3] = (self.trjfile.variables['cell_lengths'][:] * - # scale_factors['cell_lengths']) - # self.ts._unitcell[3:] = (self.trjfile.variables['cell_angles'][:] * - # scale_factors['cell_angles']) - - # # Convert units inplace - # if self.convert_units: - # self.convert_pos_from_native(self.ts._pos) - # self.convert_time_from_native(self.ts.time) - # if self.has_velocities: - # self.convert_velocities_from_native(self.ts._velocities, - # inplace=True) - # if self.has_forces: - # self.convert_forces_from_native(self.ts._forces, - # inplace=True) - # if self.periodic: - # self.convert_pos_from_native(self.ts._unitcell[:3]) From 736db88da572de781385038b291165ab552a7472 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 14:47:46 -0400 Subject: [PATCH 24/38] make NCRST work --- package/MDAnalysis/coordinates/INPCRD.py | 16 +- package/MDAnalysis/coordinates/TRJ.py | 211 +++--------------- .../MDAnalysisTests/coordinates/test_ncrst.py | 64 +++--- .../coordinates/test_netcdf.py | 13 +- .../data/Amber/ace_tip3p.ncrst | Bin 101732 -> 101732 bytes 5 files changed, 76 insertions(+), 228 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index b207ed8bdc6..ec17aec94f3 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -83,14 +83,13 @@ """ from . import base -import scipy.io.netcdf import warnings import logging +from scipy.io import netcdf_file from .timestep import Timestep -from .TRJ import NCDFMixin, NCDFPicklable from ..lib.util import store_init_arguments - +from .TRJ import NCDFPicklable, NCDFMixin logger = logging.getLogger("MDAnalysis.coordinates.AMBER") @@ -225,12 +224,13 @@ def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs): # Assign input mmap value self._mmap = mmap + super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, **kwargs) @staticmethod def parse_n_atoms(filename, **kwargs): - with scipy.io.netcdf.netcdf_file(filename, mmap=None) as f: + with scipy.io.netcdf_file(filename, mmap=None) as f: n_atoms = f.dimensions['atom'] return n_atoms @@ -251,12 +251,10 @@ def _read_first_frame(self): with NCDFPicklable(self.filename, mode='r', mmap=self._mmap, maskandscale=False) as self.trjfile: - self._check_conventions() + self._check_conventions(n_atoms=self.n_atoms) - self.n_frames = 0 - - # Single frame so we assign it to 0 - self.ts.frame = 0 + self.n_frames = 1 self._read_values(frame=()) # AMBERRESTART convention files have dimensionless datasets + self.ts.frame = 0 # 0-indexed diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 344dd2971de..7b8ca75024c 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -129,20 +129,20 @@ .. _GitHub Discussions: https://github.com/MDAnalysis/mdanalysis/discussions """ -import scipy.io.netcdf import numpy as np -import warnings -import errno -import logging from math import isclose +from scipy.io import netcdf_file import MDAnalysis from .timestep import Timestep from . import base from ..lib import util from ..lib.util import store_init_arguments -logger = logging.getLogger("MDAnalysis.coordinates.AMBER") +import warnings +import errno +import logging +logger = logging.getLogger("MDAnalysis.coordinates.AMBER") try: import netCDF4 @@ -384,9 +384,9 @@ def _check_conventions(self, n_atoms=None): try: ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') if not ConventionVersion == self.version: - wmsg = ("NCDF file format is {0!s} but the reader " - "implements format {1!s}".format( - ConventionVersion, self.version)) + wmsg = ("NCDF {0} format is {1!s} but the reader " + "implements format {2!s}".format( + file_format, ConventionVersion, self.version)) warnings.warn(wmsg) logger.warning(wmsg) except AttributeError: @@ -417,7 +417,7 @@ def _check_conventions(self, n_atoms=None): # if those attributes do not exist if not (hasattr(self.trjfile, 'program') and hasattr(self.trjfile, 'programVersion')): - wmsg = ("NCDF {0} {1} may not fully adhere to AMBER " + wmsg = ("The NCDF {0} {1} may not fully adhere to AMBER " "standards as either the `program` or `programVersion` " "attributes are missing".format(file_format, self.filename)) warnings.warn(wmsg) @@ -467,15 +467,12 @@ def _check_conventions(self, n_atoms=None): self.has_time = True except KeyError: self.has_time = False - wmsg = ("NCDF trajectory does not contain `time` information;" - " `time` will be set as an increasing index") + wmsg = ("NCDF {0} {1} does not contain `time` information;" + " `time` will be set as an increasing index".format( + file_format, self.filename)) warnings.warn(wmsg) logger.warning(wmsg) - - self._verify_units(self.trjfile.variables['coordinates'].units, - 'angstrom') - # Check for scale_factor attributes for all data variables and # store this to multiply through later (Issue #2323) self.scale_factors = {'time': None, @@ -497,6 +494,18 @@ def _check_conventions(self, n_atoms=None): "not implemented".format(variable)) raise NotImplementedError(errmsg) + # Default to length units of Angstrom + try: + self._verify_units(self.trjfile.variables['coordinates'].units, + 'angstrom') + except KeyError: + # Technically coordinate information is not required, however + # the lack of it in a restart file is highly unlikely + errmsg = ("NetCDF restart file {0} is missing coordinate " + "information ".format(self.filename)) + logger.fatal(errmsg) + raise ValueError(errmsg) + self.has_velocities = 'velocities' in self.trjfile.variables if self.has_velocities: self._verify_units(self.trjfile.variables['velocities'].units, @@ -523,7 +532,6 @@ def _check_conventions(self, n_atoms=None): reader=self, # for dt **self._ts_kwargs) - def _read_values(self, frame): ts = self.ts @@ -539,7 +547,8 @@ def _read_values(self, frame): ts._pos[:] = self._get_var_and_scale('coordinates', frame) if self.has_time: - ts.time = self._get_var_and_scale('time', frame) + time = self._get_var_and_scale('time', frame) + ts.time = time[0] if isinstance(time, (list, np.ndarray)) else time if self.has_velocities: ts._velocities[:] = self._get_var_and_scale('velocities', frame) if self.has_forces: @@ -696,170 +705,12 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): f"frame information") raise ValueError(errmsg) from None - # # AMBER NetCDF files should always have a convention - # try: - # conventions = self.trjfile.Conventions - # if not ('AMBER' in conventions.decode('utf-8').split(',') or - # 'AMBER' in conventions.decode('utf-8').split()): - # errmsg = ("NCDF trajectory {0} does not conform to AMBER " - # "specifications, " - # "http://ambermd.org/netcdf/nctraj.xhtml " - # "('AMBER' must be one of the token in attribute " - # "Conventions)".format(self.filename)) - # logger.fatal(errmsg) - # raise TypeError(errmsg) - # except AttributeError: - # errmsg = "NCDF trajectory {0} is missing Conventions".format( - # self.filename) - # logger.fatal(errmsg) - # raise ValueError(errmsg) from None - - # # AMBER NetCDF files should also have a ConventionVersion - # try: - # ConventionVersion = self.trjfile.ConventionVersion.decode('utf-8') - # if not ConventionVersion == self.version: - # wmsg = ("NCDF trajectory format is {0!s} but the reader " - # "implements format {1!s}".format( - # ConventionVersion, self.version)) - # warnings.warn(wmsg) - # logger.warning(wmsg) - # except AttributeError: - # errmsg = "NCDF trajectory {0} is missing ConventionVersion".format( - # self.filename) - # raise ValueError(errmsg) from None - - # # The AMBER NetCDF standard enforces 64 bit offsets - # if not self.trjfile.version_byte == 2: - # errmsg = ("NCDF trajectory {0} does not conform to AMBER " - # "specifications, as detailed in " - # "https://ambermd.org/netcdf/nctraj.xhtml " - # "(NetCDF file does not use 64 bit offsets " - # "[version_byte = 2])".format(self.filename)) - # logger.fatal(errmsg) - # raise TypeError(errmsg) - - # # The AMBER NetCDF standard enforces 3D coordinates - # try: - # if not self.trjfile.dimensions['spatial'] == 3: - # errmsg = "Incorrect spatial value for NCDF trajectory file" - # raise TypeError(errmsg) - # except KeyError: - # errmsg = "NCDF trajectory does not contain spatial dimension" - # raise ValueError(errmsg) from None - - # # AMBER NetCDF specs require program and programVersion. Warn users - # # if those attributes do not exist - # if not (hasattr(self.trjfile, 'program') and - # hasattr(self.trjfile, 'programVersion')): - # wmsg = ("NCDF trajectory {0} may not fully adhere to AMBER " - # "standards as either the `program` or `programVersion` " - # "attributes are missing".format(self.filename)) - # warnings.warn(wmsg) - # logger.warning(wmsg) - - # try: - # self.n_atoms = self.trjfile.dimensions['atom'] - # if n_atoms is not None and n_atoms != self.n_atoms: - # errmsg = ("Supplied n_atoms ({0}) != natom from ncdf ({1}). " - # "Note: n_atoms can be None and then the ncdf value " - # "is used!".format(n_atoms, self.n_atoms)) - # raise ValueError(errmsg) - # except KeyError: - # errmsg = ("NCDF trajectory {0} does not contain atom " - # "information".format(self.filename)) - # raise ValueError(errmsg) from None - - # try: - # self.n_frames = self.trjfile.dimensions['frame'] - # # example trajectory when read with scipy.io.netcdf has - # # dimensions['frame'] == None (indicating a record dimension that - # # can grow) whereas if read with netCDF4 I get - # # len(dimensions['frame']) == 10: in any case, we need to get - # # the number of frames from somewhere such as the time variable: - # if self.n_frames is None: - # self.n_frames = self.trjfile.variables['coordinates'].shape[0] - # except KeyError: - # errmsg = (f"NCDF trajectory {self.filename} does not contain " - # f"frame information") - # raise ValueError(errmsg) from None - - # try: - # self.remarks = self.trjfile.title - # except AttributeError: - # self.remarks = "" - # # other metadata (*= requd): - # # - application AMBER - # # - - # # checks for not-implemented features (other units would need to be - # # hacked into MDAnalysis.units) - # try: - # self._verify_units(self.trjfile.variables['time'].units, 'picosecond') - # self.has_time = True - # except KeyError: - # self.has_time = False - # wmsg = ("NCDF trajectory does not contain `time` information;" - # " `time` will be set as an increasing index") - # warnings.warn(wmsg) - # logger.warning(wmsg) - - - # self._verify_units(self.trjfile.variables['coordinates'].units, - # 'angstrom') - - # # Check for scale_factor attributes for all data variables and - # # store this to multiply through later (Issue #2323) - # self.scale_factors = {'time': None, - # 'cell_lengths': None, - # 'cell_angles': None, - # 'coordinates': None, - # 'velocities': None, - # 'forces': None} - - # for variable in self.trjfile.variables: - # if hasattr(self.trjfile.variables[variable], 'scale_factor'): - # if variable in self.scale_factors: - # scale_factor = self.trjfile.variables[variable].scale_factor - # if not isinstance(scale_factor, (float, np.floating)): - # raise TypeError(f"{scale_factor} is not a float") - # self.scale_factors[variable] = scale_factor - # else: - # errmsg = ("scale_factors for variable {0} are " - # "not implemented".format(variable)) - # raise NotImplementedError(errmsg) - - # self.has_velocities = 'velocities' in self.trjfile.variables - # if self.has_velocities: - # self._verify_units(self.trjfile.variables['velocities'].units, - # 'angstrom/picosecond') - - # self.has_forces = 'forces' in self.trjfile.variables - # if self.has_forces: - # self._verify_units(self.trjfile.variables['forces'].units, - # 'kilocalorie/mole/angstrom') - - # self.periodic = 'cell_lengths' in self.trjfile.variables - # if self.periodic: - # self._verify_units(self.trjfile.variables['cell_lengths'].units, - # 'angstrom') - # # As of v1.0.0 only `degree` is accepted as a unit - # cell_angle_units = self.trjfile.variables['cell_angles'].units - # self._verify_units(cell_angle_units, 'degree') - - # self._current_frame = 0 - - # self.ts = self._Timestep(self.n_atoms, - # velocities=self.has_velocities, - # forces=self.has_forces, - # reader=self, # for dt - # **self._ts_kwargs) - # load first data frame self._read_frame(0) @staticmethod def parse_n_atoms(filename, **kwargs): - with scipy.io.netcdf_file(filename, mmap=None) as f: + with netcdf_file(filename, mmap=None) as f: n_atoms = f.dimensions['atom'] return n_atoms @@ -1155,9 +1006,9 @@ def _init_netcdf(self, periodic=True): ncfile = netCDF4.Dataset(self.filename, 'w', format='NETCDF3_64BIT') else: - ncfile = scipy.io.netcdf_file(self.filename, - mode='w', version=2, - maskandscale=False) + ncfile = netcdf_file(self.filename, + mode='w', version=2, + maskandscale=False) wmsg = ("Could not find netCDF4 module. Falling back to MUCH " "slower scipy.io.netcdf implementation for writing.") logger.warning(wmsg) @@ -1381,7 +1232,7 @@ def close(self): self.trjfile = None -class NCDFPicklable(scipy.io.netcdf_file): +class NCDFPicklable(netcdf_file): """NetCDF file object (read-only) that can be pickled. This class provides a file-like object (as returned by diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py index 68aa54eb153..e3ffdea6b7e 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -23,7 +23,7 @@ from __future__ import absolute_import import MDAnalysis as mda import numpy as np -from scipy.io import netcdf +from scipy.io import netcdf_file from MDAnalysis.coordinates.INPCRD import NCRSTReader import pytest from numpy.testing import ( @@ -118,20 +118,21 @@ class TestReadACEBox(_NCRestartTest): def test_positions_resid1(self, universe): ag = universe.select_atoms('resid 1') - expected = np.array([[16.91830635, 11.8711319, 15.46306515], - [16.02449417, 12.34413528, 15.86983871], - [16.05173683, 12.2475071, 16.95520592], - [15.09445763, 12.00988102, 15.41004944], - [16.09916306, 13.7953701, 15.57103825], - [16.00987625, 14.24524307, 14.39752007]], + expected = np.array([[15.24987316, 12.57817841, 15.19173145], + [14.92551136, 13.58887959, 14.94400883], + [15.28570271, 14.3409605 , 15.64596176], + [13.8408432 , 13.63474751, 15.04143524], + [15.29404449, 14.23300934, 13.60826206], + [14.43975544, 14.56124306, 12.85594559]], dtype=np.float32) assert_almost_equal(expected, ag.positions, self.prec) def test_positions_resid42(self, universe): ag = universe.select_atoms('resid 42') - expected = np.array([[20.67843246, 21.18344688, 20.79789162], - [19.85808182, 21.5282135, 21.15058327], - [20.97104073, 20.54719162, 21.45041847]], + + expected = np.array([[21.78003883, 21.15958595, 19.864048], + [20.85104752, 21.08408165, 20.08200645], + [22.18930817, 20.41044617, 20.29708672]], dtype=np.float32) assert_almost_equal(expected, ag.positions, self.prec) @@ -150,7 +151,7 @@ class _NCRSTGenerator(object): def create_ncrst(self, params): # Create under context manager - with netcdf.netcdf_file(params['filename'], mode='w', + with netcdf_file(params['filename'], mode='w', version=params['version_byte']) as ncrst: # Top level attributes if params['Conventions']: @@ -249,7 +250,7 @@ def test_attribute_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) - with pytest.raises(AttributeError): + with pytest.raises(ValueError): NCRSTReader(params['filename']) @pytest.mark.parametrize('key,value', ( @@ -261,7 +262,7 @@ def test_key_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) - with pytest.raises(KeyError): + with pytest.raises(ValueError): NCRSTReader(params['filename']) @pytest.mark.parametrize('key,value', ( @@ -275,16 +276,16 @@ def test_not_implemented_errors(self, tmpdir, key, value): with pytest.raises(NotImplementedError): NCRSTReader(params['filename']) - @pytest.mark.parametrize('value', [ - 'time', 'coordinates', 'spatial', - 'velocities', 'forces' - ]) - def test_scale_factor(self, tmpdir, value): - params = self.gen_params(key='scale_factor', value=value) - with tmpdir.as_cwd(): - self.create_ncrst(params) - with pytest.raises(NotImplementedError): - NCRSTReader(params['filename']) + # @pytest.mark.parametrize('value', [ + # 'time', 'coordinates', 'spatial', + # 'velocities', 'forces' + # ]) + # def test_scale_factor(self, tmpdir, value): + # params = self.gen_params(key='scale_factor', value=value) + # with tmpdir.as_cwd(): + # self.create_ncrst(params) + # with pytest.raises(NotImplementedError): + # NCRSTReader(params['filename']) def test_conventionversion_warn(self, tmpdir): params = self.gen_params(key='ConventionVersion', value='2.0') @@ -294,7 +295,7 @@ def test_conventionversion_warn(self, tmpdir): NCRSTReader(params['filename']) assert len(record) == 1 - wmsg = "NCRST format is 2.0 but the reader implements format 1.0" + wmsg = "NCDF restart file format is 2.0 but the reader implements format 1.0" assert str(record[0].message.args[0]) == wmsg @pytest.mark.parametrize('key,value', ( @@ -309,9 +310,9 @@ def test_program_warn(self, tmpdir, key, value): NCRSTReader(params['filename']) assert len(record) == 1 - wmsg = ("This NCRST file may not fully adhere to AMBER " + wmsg = ("This NCDF restart file {0} may not fully adhere to AMBER " "standards as either the `program` or `programVersion` " - "attributes are missing") + "attributes are missing".format(params['filename'])) assert str(record[0].message.args[0]) == wmsg def test_notime_warn(self, tmpdir): @@ -322,11 +323,10 @@ def test_notime_warn(self, tmpdir): NCRSTReader(params['filename']) # Lack of time triggers two warnings - assert len(record) == 2 - wmsg1 = ("NCRestart file {0} does not contain time information. " - "This should be expected if the file was not created " - "from an MD trajectory (e.g. a minimization)".format( + assert len(record) == 1 + wmsg1 = ("NCDF restart file {0} does not contain `time` information;" + " `time` will be set as an increasing index".format( params['filename'])) assert str(record[0].message.args[0]) == wmsg1 - wmsg2 = ("Reader has no dt information, set to 1.0 ps") - assert str(record[1].message.args[0]) == wmsg2 + #wmsg2 = ("Reader has no dt information, set to 1.0 ps") + #assert str(record[1].message.args[0]) == wmsg2 diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index a3085a80564..b756814acd8 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -23,7 +23,6 @@ import MDAnalysis as mda import numpy as np import sys - from scipy.io import netcdf_file import pytest @@ -387,7 +386,7 @@ def test_warn_user_no_time_information(self, u): "NCDF trajectory does not contain `time` information;" " `time` will be set as an increasing index" ) - with pytest.warns(UserWarning, match=wmsg): + with pytest.warns(UserWarning, match=wmsg[0]): u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) @@ -778,7 +777,7 @@ def test_conventionversion_warn(self, tmpdir): assert len(record) == 1 wmsg = ( - "NCDF file format is 2.0 but the reader " + "NCDF trajectory format is 2.0 but the reader " "implements format 1.0" ) assert str(record[0].message.args[0]) == wmsg @@ -795,7 +794,7 @@ def test_program_warn(self, tmpdir, mutation): assert len(record) == 1 wmsg = ( - "NCDF trajectory test.nc may not fully adhere to AMBER " + "The NCDF trajectory test.nc may not fully adhere to AMBER " "standards as either the `program` or `programVersion` " "attributes are missing" ) @@ -853,9 +852,9 @@ def _test_write_trajectory(self, universe, outfile): # which should be "float32". # See http://docs.scipy.org/doc/numpy-1.10.0/reference/arrays.dtypes.html # and https://github.com/MDAnalysis/mdanalysis/pull/503 - dataset = netcdf_file(outfile, "r") - coords = dataset.variables["coordinates"] - time = dataset.variables["time"] + with netcdf_file(outfile, "r") as dataset: + coords = dataset.variables["coordinates"][...] + time = dataset.variables["time"][...] assert_equal( coords[:].dtype.name, np.dtype(np.float32).name, diff --git a/testsuite/MDAnalysisTests/data/Amber/ace_tip3p.ncrst b/testsuite/MDAnalysisTests/data/Amber/ace_tip3p.ncrst index ca091fde6e72fdb22fa96773742d2051fd80d36d..48ccf477f5dd0cef5f6464d2922e891c3500f1d7 100644 GIT binary patch literal 101732 zcma&v2Xqu=-~a#6AtWKakalf)*=)AV&hCbi3qd;4dmBpVolq4RX(G~lXDCvYsvsaR z^d=otqzy$W(m_Be{;tn=xc|@df6nhY=f^qTue`rAnVp@s5z)J9wdzIv%wPV365_8? 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zoT%*LlU-eQ{#&yhTHU{$M=LKrNTqntT8HNDy+&Z@Xv{^nRu21~Exs##N^2sou%V_r za+$4p8}4FDqq8+Gt(-Q@SXxs5b0S7gw=mb(jfVtEY`)npL;HQ14(HW3Hsc(Bm+nbp z&B50!cJ-~64JCF_0~dzBuG((8qWHLj#@{JlW30@)(n5z$zaM8qy|Rrt4&i!xY>9om zwM)xy-DA2z+5Hw;i_PM}^I{8!nR)(4W-d_+HnGEh+`Wk6@7?TDDBbTnWjb=qn;tuR zc!>qIa^dv?Lq~Oy!*287BxB&NE2(tMSmHq~EB(-7r$ui7IB(bXwb_MPty~)W$RQ8n z_03)uJLTQ^E<54RWOnG6&NBt#_Yj|_TD0_Kk7j-GxUsOjfsGC=@m4!fVxAu4LCybk zrLaq@`q=DH-7be#9Bt)6>AK-8Tk@KH;zCUe&Ij1P&vu{^C>@8?c4q&O+AF3z zXi58ShS1bW_uEh_zN=qPF{fU3(4iAsDlE&P|AKjWNb9K{&x9tT!-_5q?I1+T6~bL z$*ab(HFo87#^iT%9d^|X(+&(Bmj?j;9^sb9Y^d?K z#yC)Nn$Hv(eN}-%%|8DbTiYj??<3Vsx3lrSvl9+2imX4r`2uD?)WUA>V2tBqY>fx; zxdMHuBpht3?8+@s0O!}g*4t2WCQmiyHVV+to=0m0N_0j;i>77|2iR}o9;8~ZpjhDG zA-6XeJmUW0gNFAu;sduQ!?d72Va5j I@&Eb%0N*2mCIA2c From 2ab9fe16f5ce7536a98efce4fbaa679ed3481ae5 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 14:48:05 -0400 Subject: [PATCH 25/38] typo in SingleFrameReaderBase --- package/MDAnalysis/coordinates/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index 61afa29e7da..1ae9aebec42 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1666,7 +1666,7 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs): self.convert_units = convert_units self.n_frames = 1 - self.n_atom = n_atoms + self.n_atoms = n_atoms ts_kwargs = {} for att in ('dt', 'time_offset'): From 5bf1ce0c6a95723b3ed59f28ba8db8404668e06a Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 14:53:55 -0400 Subject: [PATCH 26/38] Revert "typo in SingleFrameReaderBase" This reverts commit 2ab9fe16f5ce7536a98efce4fbaa679ed3481ae5. --- package/MDAnalysis/coordinates/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index 1ae9aebec42..61afa29e7da 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1666,7 +1666,7 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs): self.convert_units = convert_units self.n_frames = 1 - self.n_atoms = n_atoms + self.n_atom = n_atoms ts_kwargs = {} for att in ('dt', 'time_offset'): From 614f9f6d2f10148fb201e4e096bb1b4fae088e5a Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 15:04:05 -0400 Subject: [PATCH 27/38] black lint --- package/MDAnalysis/coordinates/INPCRD.py | 55 +++++++++++++----------- 1 file changed, 31 insertions(+), 24 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index ec17aec94f3..1fa06bbbf5e 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -94,7 +94,6 @@ logger = logging.getLogger("MDAnalysis.coordinates.AMBER") - class INPReader(base.SingleFrameReaderBase): """Reader for Amber restart files. @@ -108,8 +107,8 @@ class INPReader(base.SingleFrameReaderBase): """ - format = ['INPCRD', 'RESTRT', 'RST7'] - units = {'length': 'Angstrom'} + format = ["INPCRD", "RESTRT", "RST7"] + units = {"length": "Angstrom"} def _read_first_frame(self): # Read header @@ -209,52 +208,60 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin): .. versionadded: 2.10.0 """ - format = ['NCRST', 'NCRESTRT', 'NCRST7'] + format = ["NCRST", "NCRESTRT", "NCRST7"] version = "1.0" - units = {'time': 'ps', - 'length': 'Angstrom', - 'velocity': 'Angstrom/ps', - 'force': 'kcal/(mol*Angstrom)'} - + units = { + "time": "ps", + "length": "Angstrom", + "velocity": "Angstrom/ps", + "force": "kcal/(mol*Angstrom)", + } _Timestep = Timestep @store_init_arguments - def __init__(self, filename, n_atoms=None, convert_units=None, mmap=None, - **kwargs): + def __init__( + self, filename, n_atoms=None, convert_units=None, mmap=None, **kwargs + ): # Assign input mmap value self._mmap = mmap - super(NCRSTReader, self).__init__(filename, convert_units, n_atoms, - **kwargs) + super(NCRSTReader, self).__init__( + filename, convert_units, n_atoms, **kwargs + ) @staticmethod def parse_n_atoms(filename, **kwargs): with scipy.io.netcdf_file(filename, mmap=None) as f: - n_atoms = f.dimensions['atom'] + n_atoms = f.dimensions["atom"] return n_atoms @staticmethod def _verify_units(eval_units, expected_units): - if eval_units.decode('utf-8') != expected_units: - errmsg = ("NCRSTReader currently assumes that the trajectory " - "was written in units of {0} instead of {1}".format( - eval_units.decode('utf-8'), expected_units)) + if eval_units.decode("utf-8") != expected_units: + errmsg = ( + "NCRSTReader currently assumes that the trajectory " + "was written in units of {0} instead of {1}".format( + eval_units.decode("utf-8"), expected_units + ) + ) raise NotImplementedError(errmsg) def _read_first_frame(self): - """Function to read NetCDF restart file and fill timestep - """ + """Function to read NetCDF restart file and fill timestep""" # Open netcdf file via context manager # ensure maskandscale is off so we don't end up double scaling - with NCDFPicklable(self.filename, mode='r', mmap=self._mmap, - maskandscale=False) as self.trjfile: + with NCDFPicklable( + self.filename, mode="r", mmap=self._mmap, maskandscale=False + ) as self.trjfile: self._check_conventions(n_atoms=self.n_atoms) self.n_frames = 1 - self._read_values(frame=()) # AMBERRESTART convention files have dimensionless datasets + self._read_values( + frame=() + ) # AMBERRESTART convention files have dimensionless datasets - self.ts.frame = 0 # 0-indexed + self.ts.frame = 0 # 0-indexed From bf689542b93151757d24a0ed792d1cb93f7e0f7d Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 15:15:51 -0400 Subject: [PATCH 28/38] Reapply "typo in SingleFrameReaderBase" This reverts commit 5bf1ce0c6a95723b3ed59f28ba8db8404668e06a. --- package/MDAnalysis/coordinates/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index 61afa29e7da..1ae9aebec42 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1666,7 +1666,7 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs): self.convert_units = convert_units self.n_frames = 1 - self.n_atom = n_atoms + self.n_atoms = n_atoms ts_kwargs = {} for att in ('dt', 'time_offset'): From 264215f0b01e7a99957ce560e5eafa523a89960b Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 27 May 2025 15:24:08 -0400 Subject: [PATCH 29/38] black lint --- .../MDAnalysisTests/coordinates/test_ncrst.py | 253 ++++++++++-------- .../coordinates/test_netcdf.py | 2 +- testsuite/MDAnalysisTests/datafiles.py | 2 +- 3 files changed, 139 insertions(+), 118 deletions(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py index e3ffdea6b7e..cc565acfe30 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -26,18 +26,16 @@ from scipy.io import netcdf_file from MDAnalysis.coordinates.INPCRD import NCRSTReader import pytest -from numpy.testing import ( - assert_equal, - assert_almost_equal -) +from numpy.testing import assert_equal, assert_almost_equal + +from MDAnalysisTests.datafiles import PRMNCRSTbox, NCRSTbox -from MDAnalysisTests.datafiles import (PRMNCRSTbox, NCRSTbox) class _NCRestartTest(object): prec = 5 - @pytest.fixture(scope='class') + @pytest.fixture(scope="class") def universe(self): return mda.Universe(self.topology, self.filename, mmap=self.mmap) @@ -53,7 +51,7 @@ def test_mmap_value(self): assert_equal(reader._mmap, self.mmap) def test_remarks(self, universe): - title = universe.trajectory.remarks.decode('utf-8') + title = universe.trajectory.remarks.decode("utf-8") assert_equal(self.title, title) def test_n_atoms(self, universe): @@ -91,8 +89,12 @@ def test_dt(self, universe): assert str(record[0].message.args[0]) == wmsg def test_units(self, universe): - units = {'time': 'ps', 'length': 'Angstrom', - 'velocity': 'Angstrom/ps', 'force': 'kcal/(mol*Angstrom)'} + units = { + "time": "ps", + "length": "Angstrom", + "velocity": "Angstrom/ps", + "force": "kcal/(mol*Angstrom)", + } assert_equal(universe.trajectory.units, units) def test_has_velocities(self, universe): @@ -108,7 +110,7 @@ class TestReadACEBox(_NCRestartTest): # Placeholder values topology = PRMNCRSTbox filename = NCRSTbox - title = 'Cpptraj Generated Restart' + title = "Cpptraj Generated Restart" n_atoms = 1398 n_res = 465 time = 1.0 @@ -117,25 +119,34 @@ class TestReadACEBox(_NCRestartTest): mmap = None def test_positions_resid1(self, universe): - ag = universe.select_atoms('resid 1') - expected = np.array([[15.24987316, 12.57817841, 15.19173145], - [14.92551136, 13.58887959, 14.94400883], - [15.28570271, 14.3409605 , 15.64596176], - [13.8408432 , 13.63474751, 15.04143524], - [15.29404449, 14.23300934, 13.60826206], - [14.43975544, 14.56124306, 12.85594559]], - dtype=np.float32) + ag = universe.select_atoms("resid 1") + expected = np.array( + [ + [15.24987316, 12.57817841, 15.19173145], + [14.92551136, 13.58887959, 14.94400883], + [15.28570271, 14.3409605, 15.64596176], + [13.8408432, 13.63474751, 15.04143524], + [15.29404449, 14.23300934, 13.60826206], + [14.43975544, 14.56124306, 12.85594559], + ], + dtype=np.float32, + ) assert_almost_equal(expected, ag.positions, self.prec) def test_positions_resid42(self, universe): - ag = universe.select_atoms('resid 42') - - expected = np.array([[21.78003883, 21.15958595, 19.864048], - [20.85104752, 21.08408165, 20.08200645], - [22.18930817, 20.41044617, 20.29708672]], - dtype=np.float32) + ag = universe.select_atoms("resid 42") + + expected = np.array( + [ + [21.78003883, 21.15958595, 19.864048], + [20.85104752, 21.08408165, 20.08200645], + [22.18930817, 20.41044617, 20.29708672], + ], + dtype=np.float32, + ) assert_almost_equal(expected, ag.positions, self.prec) + # def test_velocities(self, universe, selstr, expected): # ag = universe.select_atoms(selstr) # assert_almost_equal(expected, ag.velocities, self.prec) @@ -151,57 +162,68 @@ class _NCRSTGenerator(object): def create_ncrst(self, params): # Create under context manager - with netcdf_file(params['filename'], mode='w', - version=params['version_byte']) as ncrst: + with netcdf_file( + params["filename"], mode="w", version=params["version_byte"] + ) as ncrst: # Top level attributes - if params['Conventions']: - setattr(ncrst, 'Conventions', params['Conventions']) - if params['ConventionVersion']: - setattr(ncrst, 'ConventionVersion', - params['ConventionVersion']) - if params['program']: - setattr(ncrst, 'program', params['program']) - if params['programVersion']: - setattr(ncrst, 'programVersion', params['programVersion']) + if params["Conventions"]: + setattr(ncrst, "Conventions", params["Conventions"]) + if params["ConventionVersion"]: + setattr( + ncrst, "ConventionVersion", params["ConventionVersion"] + ) + if params["program"]: + setattr(ncrst, "program", params["program"]) + if params["programVersion"]: + setattr(ncrst, "programVersion", params["programVersion"]) # Dimensions - if params['n_atoms']: - ncrst.createDimension('atom', params['n_atoms']) - if params['spatial']: - ncrst.createDimension('spatial', params['spatial']) - if params['time']: - ncrst.createDimension('time', 1) + if params["n_atoms"]: + ncrst.createDimension("atom", params["n_atoms"]) + if params["spatial"]: + ncrst.createDimension("spatial", params["spatial"]) + if params["time"]: + ncrst.createDimension("time", 1) # Variables - if params['time']: - time = ncrst.createVariable('time', 'd', ('time',)) - setattr(time, 'units', params['time']) + if params["time"]: + time = ncrst.createVariable("time", "d", ("time",)) + setattr(time, "units", params["time"]) time[:] = 1.0 # Spatial or atom dependent variables - if (params['spatial']) and (params['n_atoms']): - if params['coords']: - coords = ncrst.createVariable('coordinates', 'f8', - ('atom', 'spatial')) - setattr(coords, 'units', params['coords']) - coords[:] = np.asarray(range(params['spatial']), - dtype=np.float32) - spatial = ncrst.createVariable('spatial', 'c', ('spatial',)) - spatial[:] = np.asarray(list('xyz')[:params['spatial']]) - velocs = ncrst.createVariable('velocities', 'f8', - ('atom', 'spatial')) - setattr(velocs, 'units', 'angstrom/picosecond') - velocs[:] = np.asarray(range(params['spatial']), - dtype=np.float32) - forces = ncrst.createVariable('forces', 'f8', - ('atom', 'spatial')) - setattr(forces, 'units', 'kilocalorie/mole/angstrom') - forces[:] = np.asarray(range(params['spatial']), - dtype=np.float32) + if (params["spatial"]) and (params["n_atoms"]): + if params["coords"]: + coords = ncrst.createVariable( + "coordinates", "f8", ("atom", "spatial") + ) + setattr(coords, "units", params["coords"]) + coords[:] = np.asarray( + range(params["spatial"]), dtype=np.float32 + ) + spatial = ncrst.createVariable("spatial", "c", ("spatial",)) + spatial[:] = np.asarray(list("xyz")[: params["spatial"]]) + velocs = ncrst.createVariable( + "velocities", "f8", ("atom", "spatial") + ) + setattr(velocs, "units", "angstrom/picosecond") + velocs[:] = np.asarray( + range(params["spatial"]), dtype=np.float32 + ) + forces = ncrst.createVariable( + "forces", "f8", ("atom", "spatial") + ) + setattr(forces, "units", "kilocalorie/mole/angstrom") + forces[:] = np.asarray( + range(params["spatial"]), dtype=np.float32 + ) # self.scale_factor overrides which variable gets a scale_factor - if params['scale_factor']: - setattr(ncrst.variables[params['scale_factor']], - 'scale_factor', 2.0) + if params["scale_factor"]: + setattr( + ncrst.variables[params["scale_factor"]], + "scale_factor", + 2.0, + ) def gen_params(self, key=None, value=None): """Generate writer parameters, key and value can be used to overwrite @@ -209,17 +231,17 @@ def gen_params(self, key=None, value=None): """ params = { - 'filename': 'test.ncrst', - 'version_byte': 2, - 'Conventions': 'AMBERRESTART', - 'ConventionVersion': '1.0', - 'program': 'mda test_writer', - 'programVersion': 'V42', - 'n_atoms': 1, - 'spatial': 3, - 'coords': 'angstrom', - 'time': 'picosecond', - 'scale_factor': None + "filename": "test.ncrst", + "version_byte": 2, + "Conventions": "AMBERRESTART", + "ConventionVersion": "1.0", + "program": "mda test_writer", + "programVersion": "V42", + "n_atoms": 1, + "spatial": 3, + "coords": "angstrom", + "time": "picosecond", + "scale_factor": None, } if key: @@ -230,51 +252,46 @@ def gen_params(self, key=None, value=None): class TestNCRSTReaderExceptionsWarnings(_NCRSTGenerator): - @pytest.mark.parametrize('key,value', ( - ('version_byte', 1), - ('Conventions', 'Foo'), - ('spatial', 2) - )) + @pytest.mark.parametrize( + "key,value", + (("version_byte", 1), ("Conventions", "Foo"), ("spatial", 2)), + ) def test_read_type_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.raises(TypeError): - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) - @pytest.mark.parametrize('key,value', ( - ('Conventions', None), - ('ConventionVersion', None) - )) + @pytest.mark.parametrize( + "key,value", (("Conventions", None), ("ConventionVersion", None)) + ) def test_attribute_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.raises(ValueError): - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) - @pytest.mark.parametrize('key,value', ( - ('spatial', None), - ('n_atoms', None), - ('coords', None) - )) + @pytest.mark.parametrize( + "key,value", (("spatial", None), ("n_atoms", None), ("coords", None)) + ) def test_key_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.raises(ValueError): - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) - @pytest.mark.parametrize('key,value', ( - ('time', 'femtosecond'), - ('coords', 'nanometer') - )) + @pytest.mark.parametrize( + "key,value", (("time", "femtosecond"), ("coords", "nanometer")) + ) def test_not_implemented_errors(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.raises(NotImplementedError): - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) # @pytest.mark.parametrize('value', [ # 'time', 'coordinates', 'spatial', @@ -288,45 +305,49 @@ def test_not_implemented_errors(self, tmpdir, key, value): # NCRSTReader(params['filename']) def test_conventionversion_warn(self, tmpdir): - params = self.gen_params(key='ConventionVersion', value='2.0') + params = self.gen_params(key="ConventionVersion", value="2.0") with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.warns(UserWarning) as record: - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) assert len(record) == 1 wmsg = "NCDF restart file format is 2.0 but the reader implements format 1.0" assert str(record[0].message.args[0]) == wmsg - @pytest.mark.parametrize('key,value', ( - ('program', None), - ('programVersion', None) - )) + @pytest.mark.parametrize( + "key,value", (("program", None), ("programVersion", None)) + ) def test_program_warn(self, tmpdir, key, value): params = self.gen_params(key=key, value=value) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.warns(UserWarning) as record: - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) assert len(record) == 1 - wmsg = ("This NCDF restart file {0} may not fully adhere to AMBER " - "standards as either the `program` or `programVersion` " - "attributes are missing".format(params['filename'])) + wmsg = ( + "This NCDF restart file {0} may not fully adhere to AMBER " + "standards as either the `program` or `programVersion` " + "attributes are missing".format(params["filename"]) + ) assert str(record[0].message.args[0]) == wmsg def test_notime_warn(self, tmpdir): - params = self.gen_params(key='time', value=None) + params = self.gen_params(key="time", value=None) with tmpdir.as_cwd(): self.create_ncrst(params) with pytest.warns(UserWarning) as record: - NCRSTReader(params['filename']) + NCRSTReader(params["filename"]) # Lack of time triggers two warnings assert len(record) == 1 - wmsg1 = ("NCDF restart file {0} does not contain `time` information;" - " `time` will be set as an increasing index".format( - params['filename'])) + wmsg1 = ( + "NCDF restart file {0} does not contain `time` information;" + " `time` will be set as an increasing index".format( + params["filename"] + ) + ) assert str(record[0].message.args[0]) == wmsg1 - #wmsg2 = ("Reader has no dt information, set to 1.0 ps") - #assert str(record[1].message.args[0]) == wmsg2 + # wmsg2 = ("Reader has no dt information, set to 1.0 ps") + # assert str(record[1].message.args[0]) == wmsg2 diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index b756814acd8..f39415c2834 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -390,7 +390,7 @@ def test_warn_user_no_time_information(self, u): u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) -#class TestNCDFReader5(object): +# class TestNCDFReader5(object): # """NCRST Restart File with positions and forces, exported by CPPTRAJ. # # Contributed by Jeremy M. G. Leung diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 8b4a6b70bd8..1097582c3fd 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -194,7 +194,7 @@ "PRMNCRST", # Amber topology for ncrst with positions/forces/velocities "TRJNCRST", # Amber ncrst with positions/forces/velocties "PRMNCRSTbox", - "NCRSTbox", + "NCRSTbox", "PRM_NCBOX", "TRJ_NCBOX", # Amber parm7 + nc w/ pos/forces/vels/box "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) From 6613a27e6bab203995232f0f84255d275c2d137f Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 12 Jun 2025 12:38:45 -0400 Subject: [PATCH 30/38] fix tests --- package/MDAnalysis/coordinates/TRJ.py | 9 ++++++--- testsuite/MDAnalysisTests/coordinates/test_ncrst.py | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 7b8ca75024c..9e06aa6009a 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -1227,9 +1227,12 @@ def _write_next_timestep(self, ts): self.curr_frame += 1 def close(self): - if self.trjfile is not None: - self.trjfile.close() - self.trjfile = None + try: + if self.trjfile is not None: + self.trjfile.close() + self.trjfile = None + except AttributeError: + pass class NCDFPicklable(netcdf_file): diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py index cc565acfe30..69ffdcc3688 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -327,7 +327,7 @@ def test_program_warn(self, tmpdir, key, value): assert len(record) == 1 wmsg = ( - "This NCDF restart file {0} may not fully adhere to AMBER " + "The NCDF restart file {0} may not fully adhere to AMBER " "standards as either the `program` or `programVersion` " "attributes are missing".format(params["filename"]) ) From eca17ab4934a12227ae56cf643e90707ffc81317 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Thu, 26 Jun 2025 10:34:17 +0800 Subject: [PATCH 31/38] fix docstring --- package/MDAnalysis/coordinates/INPCRD.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 1fa06bbbf5e..6a53df73ceb 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -102,7 +102,7 @@ class INPReader(base.SingleFrameReaderBase): * Box information is not read (or checked for). * Velocities are currently *not supported*. - .. versionchanged: 0.20.0 + .. versionchanged: 2.10.0 Now automatically detects files with .rst7 extension. """ From b44df737967fa1a3bb3b82ef979f2ae6ea134e1b Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 22 Jul 2025 16:19:24 -0400 Subject: [PATCH 32/38] typo and doc-links fix --- package/MDAnalysis/coordinates/INPCRD.py | 10 +++++----- package/MDAnalysis/coordinates/__init__.py | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 6a53df73ceb..944860f5b51 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -22,7 +22,7 @@ # -"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD` +"""AMBER coordinate/restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD` ================================================================================ AMBER_ can write :ref:`ASCII restart` ("inpcrd") and @@ -76,7 +76,7 @@ .. Links .. _AMBER: http://ambermd.org -.. _AMBER INPCRD FORMAT: http://ambermd.org/formats.html#restart +.. _AMBER INPCRD FORMAT: https://ambermd.org/FileFormats.php#restart .. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml .. _NetCDF: http://www.unidata.ucar.edu/software/netcdf @@ -158,7 +158,7 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin): """Reader for `AMBER NETCDF format`_ (version 1.0 rev C) restart files. This reader is a :class:`SingleFrameReaderBase` adaptation of the - :class:`NCDFReader` AMBER NETCDF trajectory reader. + :class:`~MDAnalysis.coordinates.TRJ.NCDFReader` AMBER NETCDF trajectory reader. AMBER binary restart files are automatically recognised by the file extensions ".ncrst", ".ncrestrt", and ".ncrst7". @@ -201,8 +201,8 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin): See Also -------- - :class:`NCDFReader` - :class:`NCDFWriter` + :class:`~MDAnalysis.coordinates.TRJ.NCDFReader` + :class:`~MDAnalysis.coordinates.TRJ.NCDFWriter` .. versionadded: 2.10.0 diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index b1aa0a01c42..901844264f8 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -215,7 +215,7 @@ class can choose an appropriate reader automatically. | | | | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`| +---------------+-----------+-------+------------------------------------------------------+ | AMBER | ncrst, | r | binary (NetCDF) restart file | - | | ncrestrt, | | Module :mod:`MDAnalysis.coordinates.INPCRD | + | | ncrestrt, | | Module :mod:`MDAnalysis.coordinates.INPCRD` | | | ncrst7 | | | +---------------+-----------+-------+------------------------------------------------------+ | Brookhaven | pdb/ent | r/w | a relaxed PDB format (as used in MD simulations) | From 32848f458bfc15f343d1e947dcced559511cf944 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 22 Jul 2025 16:23:28 -0400 Subject: [PATCH 33/38] doc update --- package/MDAnalysis/coordinates/INPCRD.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 944860f5b51..79d04a96c9d 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -181,7 +181,8 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin): ``[0,0,0,0,0,0]``). Support for the *mmap* keyword is available as detailed - in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. The use of + in :class:`~MDAnalysis.coordinates.TRJ.NCDFReader` and + :mod:`scipy.io.netcdf.netcdf_file`. The use of ``mmap=True`` leads to around a 2x read speed improvement in a ~ 1 million atom system (AMBER STMV benchmark). As per the :class:`NCDFReader`, the default behaviour is ``mmap=None``, which means that the default behaviour From 9262e7510cc64a0b2bc51890fff9cf5f078de4d5 Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 22 Jul 2025 16:26:21 -0400 Subject: [PATCH 34/38] n_frames now read during init --- package/MDAnalysis/coordinates/TRJ.py | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 9e06aa6009a..46296f9afd8 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -435,23 +435,6 @@ def _check_conventions(self, n_atoms=None): "information".format(file_format, self.filename)) raise ValueError(errmsg) from None - # try: - # self.n_frames = self.trjfile.dimensions['frame'] - # # example trajectory when read with scipy.io.netcdf has - # # dimensions['frame'] == None (indicating a record dimension that - # # can grow) whereas if read with netCDF4 I get - # # len(dimensions['frame']) == 10: in any case, we need to get - # # the number of frames from somewhere such as the time variable: - # if self.n_frames is None: - # self.n_frames = self.trjfile.variables['coordinates'].shape[0] - # except KeyError: - # if self.is_restart: - # self.n_frames = 1 - # else: - # errmsg = ("NCDF {file_format} {self.filename} does not contain " - # "frame information").format - # raise ValueError(errmsg) from None - try: self.remarks = self.trjfile.title except AttributeError: From ec8fd955c7576a96569a46b5810590646f3501ba Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 22 Jul 2025 16:42:14 -0400 Subject: [PATCH 35/38] update tests --- .../MDAnalysisTests/coordinates/test_ncrst.py | 21 --- .../coordinates/test_netcdf.py | 156 +++++++++--------- 2 files changed, 78 insertions(+), 99 deletions(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py index 69ffdcc3688..b36ec960237 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_ncrst.py +++ b/testsuite/MDAnalysisTests/coordinates/test_ncrst.py @@ -147,16 +147,6 @@ def test_positions_resid42(self, universe): assert_almost_equal(expected, ag.positions, self.prec) -# def test_velocities(self, universe, selstr, expected): -# ag = universe.select_atoms(selstr) -# assert_almost_equal(expected, ag.velocities, self.prec) -# -# def test_forces(self, universe, selstr, expected): -# ag = universe.select_atoms(selstr) -# # We convert from kj back to the original kcal value -# assert_almost_equal(expected, ag.forces * 4.184, self.prec) - - class _NCRSTGenerator(object): """A basic modular ncrst writer based on :class:`NCDFWriter`""" @@ -293,17 +283,6 @@ def test_not_implemented_errors(self, tmpdir, key, value): with pytest.raises(NotImplementedError): NCRSTReader(params["filename"]) - # @pytest.mark.parametrize('value', [ - # 'time', 'coordinates', 'spatial', - # 'velocities', 'forces' - # ]) - # def test_scale_factor(self, tmpdir, value): - # params = self.gen_params(key='scale_factor', value=value) - # with tmpdir.as_cwd(): - # self.create_ncrst(params) - # with pytest.raises(NotImplementedError): - # NCRSTReader(params['filename']) - def test_conventionversion_warn(self, tmpdir): params = self.gen_params(key="ConventionVersion", value="2.0") with tmpdir.as_cwd(): diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index f39415c2834..a3accca0a90 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -390,70 +390,70 @@ def test_warn_user_no_time_information(self, u): u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) -# class TestNCDFReader5(object): -# """NCRST Restart File with positions and forces, exported by CPPTRAJ. -# -# Contributed by Jeremy M. G. Leung -# """ -# -# prec = 6 -# -# @pytest.fixture(scope="class") -# def u(self): -# return mda.Universe(PRMNCRST, TRJNCRST) -# -# def test_positions(self, u): -# """Check positions on first frame""" -# u.trajectory[0] -# ref_1 = np.array( -# [ -# [-1.1455358, -2.0177484, -0.55771565], -# [-0.19042611, -2.2511053, -1.0282656], -# [0.53238064, -1.5778863, -0.56737846], -# ], -# dtype=np.float64, -# ) -# assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec) -# -# def test_velocities(self, u): -# """Check forces on first frame""" -# u.trajectory[0] -# ref_1 = np.array( -# [ -# [11.86471367, 31.22108269, -4.03538418], -# [7.36676359, -4.68035316, 1.78124952], -# [12.86675262, 1.39324546, -14.97190762], -# ], -# dtype=np.float64, -# ) -# assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec) -# -# def test_forces(self, u): -# """Check forces on first frame""" -# u.trajectory[0] -# ref_1 = np.array( -# [ -# [-9.7262249, -0.37627634, -24.79876137], -# [-32.43384552, 37.47783279, -12.45422745], -# [24.10939026, -19.80618095, -17.09523582], -# ], -# dtype=np.float64, -# ) -# assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec) -# -# def test_time(self, u): -# """Check time on first frame""" -# ref = 5.0 -# assert_almost_equal(ref, u.trajectory[0].time, self.prec) -# -# def test_dt(self, u): -# """Default 1.0 fs""" -# ref = 1.0 -# assert_almost_equal(ref, u.trajectory.dt, self.prec) -# assert_almost_equal(ref, u.trajectory.ts.dt, self.prec) -# -# def test_box(self, u): -# assert u.trajectory[0].dimensions is None +class TestNCDFReader5(object): + """NCRST Restart File with positions and forces, exported by CPPTRAJ. + + Contributed by Jeremy M. G. Leung + """ + + prec = 6 + + @pytest.fixture(scope="class") + def u(self): + return mda.Universe(PRMNCRST, TRJNCRST) + + def test_positions(self, u): + """Check positions on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [-1.1455358, -2.0177484, -0.55771565], + [-0.19042611, -2.2511053, -1.0282656], + [0.53238064, -1.5778863, -0.56737846], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec) + + def test_velocities(self, u): + """Check forces on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [11.86471367, 31.22108269, -4.03538418], + [7.36676359, -4.68035316, 1.78124952], + [12.86675262, 1.39324546, -14.97190762], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec) + + def test_forces(self, u): + """Check forces on first frame""" + u.trajectory[0] + ref_1 = np.array( + [ + [ -2.32462358, -0.0899322 , -5.9270463 ], + [ -7.7518754 , 8.95741653, -2.97663188], + [ 5.76228237, -4.73379087, -4.0858593 ], + ], + dtype=np.float64, + ) + assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec) + + def test_time(self, u): + """Check time on first frame""" + ref = 5.0 + assert_almost_equal(ref, u.trajectory[0].time, self.prec) + + def test_dt(self, u): + """Default 1.0 fs""" + ref = 1.0 + assert_almost_equal(ref, u.trajectory.dt, self.prec) + assert_almost_equal(ref, u.trajectory.ts.dt, self.prec) + + def test_box(self, u): + assert u.trajectory[0].dimensions is None class _NCDFGenerator(object): @@ -853,20 +853,20 @@ def _test_write_trajectory(self, universe, outfile): # See http://docs.scipy.org/doc/numpy-1.10.0/reference/arrays.dtypes.html # and https://github.com/MDAnalysis/mdanalysis/pull/503 with netcdf_file(outfile, "r") as dataset: - coords = dataset.variables["coordinates"][...] - time = dataset.variables["time"][...] - assert_equal( - coords[:].dtype.name, - np.dtype(np.float32).name, - err_msg="ncdf coord output not float32 " - "but {}".format(coords[:].dtype), - ) - assert_equal( - time[:].dtype.name, - np.dtype(np.float32).name, - err_msg="ncdf time output not float32 " - "but {}".format(time[:].dtype), - ) + coords = dataset.variables["coordinates"] + time = dataset.variables["time"] + assert_equal( + coords[:].dtype.name, + np.dtype(np.float32).name, + err_msg="ncdf coord output not float32 " + "but {}".format(coords[:].dtype), + ) + assert_equal( + time[:].dtype.name, + np.dtype(np.float32).name, + err_msg="ncdf time output not float32 " + "but {}".format(time[:].dtype), + ) def test_write_trajectory_netCDF4(self, universe, outfile): pytest.importorskip("netCDF4") From 444ece06111b925e45665159418142c9865c8ddc Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Tue, 22 Jul 2025 16:46:31 -0400 Subject: [PATCH 36/38] lint for test_netcdf.py --- testsuite/MDAnalysisTests/coordinates/test_netcdf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index a3accca0a90..5c099621ec8 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -433,9 +433,9 @@ def test_forces(self, u): u.trajectory[0] ref_1 = np.array( [ - [ -2.32462358, -0.0899322 , -5.9270463 ], - [ -7.7518754 , 8.95741653, -2.97663188], - [ 5.76228237, -4.73379087, -4.0858593 ], + [-2.32462358, -0.0899322, -5.9270463], + [-7.7518754, 8.95741653, -2.97663188], + [5.76228237, -4.73379087, -4.0858593], ], dtype=np.float64, ) From 44f5dd4d085df9459334a8faf72f870009ac21ab Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Mon, 13 Oct 2025 14:40:59 -0400 Subject: [PATCH 37/38] bump PR to v2.11.0 --- package/CHANGELOG | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index d2104f48e1c..d779b728a8a 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -14,10 +14,27 @@ The rules for this file: ------------------------------------------------------------------------------- + * 2.11.0 +??/??/?? jeremyleung521 + +Fixes + * + +Enhancement + * Allow NCDF reader to read Amber Restart Files with extension `.ncrst` + (Issue #5030, PR #5031) + +Changes + * + +Deprecations + * + + ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev, yuxuanzhuang, yuyuan871111, tanishy7777, jpkrowe, tulga-rdn, Gareth-elliott, hmacdope, tylerjereddy, cbouy, talagayev, - DrDomenicoMarson, amruthesht, p-j-smith, jeremyleung521 + DrDomenicoMarson, amruthesht, p-j-smith * 2.10.0 @@ -45,8 +62,6 @@ Fixes directly passing them. (Issue #3520, PR #5006) Enhancements - * Allow NCDF reader to read Amber Restart Files with extension `.ncrst` - (Issue #5030, PR #5031) * Added support for reading and processing streamed data in `coordinates.base` with new `StreamFrameIteratorSliced` and `StreamReaderBase` (Issue #4827, PR #4923) * New coordinate reader: Added `IMDReader` for reading real-time streamed From a52a5733665b1e8c67f02aacc57fd0d77175b3cb Mon Sep 17 00:00:00 2001 From: "Jeremy M. G. Leung" Date: Mon, 13 Oct 2025 14:45:07 -0400 Subject: [PATCH 38/38] Enhancements --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index d779b728a8a..ad27d4aa7ab 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -20,7 +20,7 @@ The rules for this file: Fixes * -Enhancement +Enhancements * Allow NCDF reader to read Amber Restart Files with extension `.ncrst` (Issue #5030, PR #5031)