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added atom mapping to vasp and changed 3d view atom properties table …
…so that it has the element symbol which includes the isotope
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MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py
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| # ************************************************************************** | ||
| # | ||
| # MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments | ||
| # | ||
| # @file MDANSE/Framework/Configurators/XDATCARFileConfigurator.py | ||
| # @brief Implements module/class/test VASP | ||
| # | ||
| # @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx | ||
| # @license GNU General Public License v3 or higher (see LICENSE) | ||
| # @copyright Institut Laue Langevin 2013-now | ||
| # @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now | ||
| # @authors Scientific Computing Group at ILL (see AUTHORS) | ||
| # | ||
| # ************************************************************************** | ||
| import numpy as np | ||
|
|
||
| from MDANSE.Core.Error import Error | ||
| from MDANSE.Framework.Units import measure | ||
| from MDANSE.Framework.AtomMapping import AtomLabel | ||
| from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator | ||
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| class XDATCARFileError(Error): | ||
| pass | ||
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| class XDATCARFileConfigurator(FileWithAtomDataConfigurator): | ||
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| def parse(self): | ||
| filename = self["filename"] | ||
| self["instance"] = open(filename, "rb") | ||
|
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| # Read header | ||
| self["instance"].readline() | ||
| header = [] | ||
| while True: | ||
| self._headerSize = self["instance"].tell() | ||
| line = self["instance"].readline().strip() | ||
| if not line or line.lower().startswith(b"direct"): | ||
| self._frameHeaderSize = self["instance"].tell() - self._headerSize | ||
| break | ||
| header.append(line.decode()) | ||
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| self["scale_factor"] = float(header[0]) | ||
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| cell = " ".join(header[1:4]).split() | ||
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| cell = np.array(cell, dtype=np.float64) | ||
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| self["cell_shape"] = ( | ||
| np.reshape(cell, (3, 3)) | ||
| * self["scale_factor"] | ||
| * measure(1.0, "ang").toval("nm") | ||
| ) | ||
|
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| self["atoms"] = list( | ||
| zip(header[4].split(), [int(v) for v in header[5].split()]) | ||
| ) | ||
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| self["n_atoms"] = sum([v[1] for v in self["atoms"]]) | ||
|
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| # The point here is to determine if the trajectory is NVT or NPT. If traj is NPT, the box will change at each iteration and the "header" will appear betwwen every frame | ||
| # We try to read the two first frames to figure it out | ||
| nAtoms = 0 | ||
| while True: | ||
| self._frameSize = self["instance"].tell() | ||
| line = self["instance"].readline().strip() | ||
| if not line or line.lower().startswith(b"direct"): | ||
| break | ||
| nAtoms += 1 | ||
|
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| if nAtoms == self["n_atoms"]: | ||
| # Traj is NVT | ||
| # Structure is | ||
| # Header | ||
| # FrameHeader | ||
| # Frame 1 | ||
| # FrameHeader | ||
| # Frame 2 | ||
| # ... | ||
| # With frameHeader being "dummy" | ||
| self._npt = False | ||
| self._frameSize -= self._headerSize | ||
| self._actualFrameSize = self._frameSize - self._frameHeaderSize | ||
| else: | ||
| # Traj is NPT | ||
| # Structure is | ||
| # FrameHeader | ||
| # Frame 1 | ||
| # FrameHeader | ||
| # Frame 2 | ||
| # ... | ||
| # With FrameHeader containing box size | ||
| self._npt = True | ||
| self._actualFrameSize = self._frameSize | ||
| self._frameSize -= self._headerSize | ||
| self._frameHeaderSize += self._headerSize | ||
| self._headerSize = 0 | ||
| self._actualFrameSize = self._frameSize - self._frameHeaderSize | ||
| # Retry to read the first frame | ||
| self["instance"].seek(self._frameHeaderSize) | ||
| nAtoms = 0 | ||
| while True: | ||
| self._frameSize = self["instance"].tell() | ||
| line = self["instance"].readline().strip() | ||
| if len(line.split(" ")) != 3: | ||
| break | ||
| nAtoms += 1 | ||
|
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||
| if nAtoms != self["n_atoms"]: | ||
| # Something went wrong | ||
| raise XDATCARFileError( | ||
| "The number of atoms (%d) does not match the size of a frame (%d)." | ||
| % (nAtoms, self["n_atoms"]) | ||
| ) | ||
|
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| # Read frame number | ||
| self["instance"].seek(0, 2) | ||
| self["n_frames"] = ( | ||
| self["instance"].tell() - self._headerSize | ||
| ) / self._frameSize | ||
|
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||
| # Go back to top | ||
| self["instance"].seek(0) | ||
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| def read_step(self, step): | ||
| self["instance"].seek(self._headerSize + step * self._frameSize) | ||
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| if self._npt: | ||
| # Read box size | ||
| self["instance"].readline() | ||
| header = [] | ||
| while True: | ||
| line = self["instance"].readline().strip() | ||
| if not line or line.lower().startswith("direct"): | ||
| break | ||
| header.append(line) | ||
| cell = " ".join(header[1:4]).split() | ||
| cell = np.array(cell, dtype=np.float64) | ||
| self["cell_shape"] = ( | ||
| np.reshape(cell, (3, 3)) | ||
| * self["scale_factor"] | ||
| * measure(1.0, "ang").toval("nm") | ||
| ) | ||
| else: | ||
| self["instance"].read(self._frameHeaderSize) | ||
|
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| data = np.array( | ||
| self["instance"].read(self._actualFrameSize).split(), dtype=np.float64 | ||
| ) | ||
|
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| config = np.reshape(data, (self["n_atoms"], 3)) | ||
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| return config | ||
|
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| def close(self): | ||
| self["instance"].close() | ||
|
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| def get_atom_labels(self) -> list[AtomLabel]: | ||
| """ | ||
| Returns | ||
| ------- | ||
| list[AtomLabel] | ||
| An ordered list of atom labels. | ||
| """ | ||
| labels = [] | ||
| for symbol, _ in self["atoms"]: | ||
| label = AtomLabel(symbol) | ||
| if label not in labels: | ||
| labels.append(label) | ||
| return labels |
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