DL_POLY.py 14.7 KB
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#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
#------------------------------------------------------------------------------------------
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
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#71 avenue des Martyrs
#38000 Grenoble Cedex 9
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#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
#aoun[at]ill.fr
#
#This library is free software; you can redistribute it and/or
#modify it under the terms of the GNU Lesser General Public
#License as published by the Free Software Foundation; either
#version 2.1 of the License, or (at your option) any later version.
#
#This library is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#Lesser General Public License for more details.
#
#You should have received a copy of the GNU Lesser General Public
#License along with this library; if not, write to the Free Software
#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA

''' 
Created on Apr 10, 2015

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:author: Eric C. Pellegrini
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'''

import collections
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import os
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import re

import numpy

from MMTK import Atom, AtomCluster
from MMTK import Units
from MMTK.ParticleProperties import Configuration, ParticleVector
from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput
from MMTK.Universe import InfiniteUniverse, ParallelepipedicPeriodicUniverse

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from MDANSE import ELEMENTS, REGISTRY
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from MDANSE.Core.Error import Error
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from MDANSE.Framework.Jobs.Converter import Converter
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_HISTORY_FORMAT = {}
_HISTORY_FORMAT["2"] = {"rec1" : 81, "rec2" : 31, "reci" : 61, "recii" : 37, "reciii" : 37, "reciv" : 37, "reca" : 43, "recb" : 37, "recc" : 37, "recd" : 37}
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_HISTORY_FORMAT["3"] = {"rec1" : 73, "rec2" : 73, "reci" : 73, "recii" : 73, "reciii" : 73, "reciv" : 73, "reca" : 73, "recb" : 73, "recc" : 73, "recd" : 73}
_HISTORY_FORMAT["4"] = {"rec1" : 73, "rec2" : 73, "reci" : 73, "recii" : 73, "reciii" : 73, "reciv" : 73, "reca" : 73, "recb" : 73, "recc" : 73, "recd" : 73}
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class FieldFileError(Error):
    pass          

class HistoryFileError(Error):
    pass

class DL_POLYConverterError(Error):
    pass

class FieldFile(dict):

    def __init__(self, filename, aliases):
        
        self._filename = filename
        
        self._aliases = aliases
        
        self.parse()        
        
        
    def parse(self):

        # The FIELD file is opened for reading, its contents stored into |lines| and then closed.
        unit = open(self._filename, 'r')

        # Read and remove the empty and comments lines from the contents of the FIELD file.
        lines = [line.strip() for line in unit.readlines() if line.strip() and not re.match('#',line)]
    
        # Close the FIELD file.
        unit.close()

        self['title'] = lines.pop(0)

        self['units'] = lines.pop(0)

        # Extract the number of molecular types
        _, self['n_molecular_types'] = re.match("(molecules|molecular types)\s+(\d+)",lines.pop(0), re.IGNORECASE).groups()

        self['n_molecular_types'] = int(self['n_molecular_types'])

        molBlocks = [i for i,line in enumerate(lines) if re.match("finish", line, re.IGNORECASE)]
        
        if self['n_molecular_types'] != len(molBlocks):
            raise FieldFileError("Error in the definition of the molecular types")
    
        self['molecules'] = []
    
        first = 0
    
        for last in molBlocks:
        
            moleculeName = lines[first]
        
            # Extract the number of molecular types
            nMolecules = re.match("nummols\s+(\d+)",lines[first+1], re.IGNORECASE).groups()[0]
            nMolecules = int(nMolecules)
                
            for i in range(first+2,last):
                        
                match = re.match("atoms\s+(\d+)",lines[i], re.IGNORECASE)
                if match:

                    nAtoms = int(match.groups()[0])
                
                    sumAtoms = 0
                
                    comp = i+1

                    atoms = []
                
                    while (sumAtoms < nAtoms):
                                    
                        sitnam = lines[comp][:8].strip()
                    
                        vals = lines[comp][8:].split()

                        if self._aliases.has_key(sitnam):
                            element = self._aliases[sitnam]
                        else:
                            element = sitnam
                            while 1:
                                if ELEMENTS.has_element(element):
                                    break
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                                element = element[:-1]
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                                if not element:
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                                    raise FieldFileError("Could not define any element from %r" % sitnam)
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                        try:
                            nrept = int(vals[2])
                        except IndexError:
                            nrept = 1
                    
                        atoms.extend([(sitnam,element)]*nrept)
                                            
                        sumAtoms += nrept
                        
                        comp += 1
                    
                    self['molecules'].append([moleculeName,nMolecules,atoms])
                
                    break

            first = last + 1
        
    def build_mmtk_contents(self, universe=None):
                
        self._mmtkObjects = []
            
        for moleculeName, nMolecules, atomicContents in self["molecules"]:
            
            # Loops over the number of molecules of the current type.
            for _ in range(nMolecules):
                
                # This list will contains the MMTK instance of the atoms of the molecule.
                temp = []
                
                # Loops over the atom of the molecule.
                for i, (name, element) in enumerate(atomicContents):
                    # The atom is created.
                    a = Atom(element, name="%s%s" % (name,i))
                    temp.append(a)

                if len(temp) > 1:
                    temp = [AtomCluster(temp, name=moleculeName)]               
                
                self._mmtkObjects.append(temp[0])
                    
        if universe is not None:
            [universe.addObject(obj) for obj in self._mmtkObjects]
            
class HistoryFile(dict):
    
    def __init__(self, filename, version="2"):
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        self['instance'] = open(filename, 'rb')

        testLine = len(self['instance'].readline())
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        if (testLine not in [81,82]) and (testLine not in [73,74]):
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            raise HistoryFileError('Invalid DLPOLY history file')

        self['instance'].seek(0,0)
        
        self["version"] = version
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        offset = testLine - _HISTORY_FORMAT[self["version"]]["rec1"]
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        self._headerSize = _HISTORY_FORMAT[self["version"]]["rec1"] + _HISTORY_FORMAT[self["version"]]["rec2"] + 2*offset

        self['instance'].read(_HISTORY_FORMAT[self["version"]]["rec1"]+offset)

        data = self['instance'].read(_HISTORY_FORMAT[self["version"]]["rec2"]+offset)
                                
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        self["keytrj"], self["imcon"], self["natms"] = [int(v) for v in data.split()[0:3]] 
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        if self["keytrj"] not in range(3):
            raise HistoryFileError("Invalid value for trajectory output key.")

        if self["imcon"] not in range(4):
            raise HistoryFileError("Invalid value for periodic boundary conditions key.")

        self._configHeaderSize = _HISTORY_FORMAT[self["version"]]["reci"] + 3*_HISTORY_FORMAT[self["version"]]["recii"] + 4*offset
        
        self._configSize = (_HISTORY_FORMAT[self["version"]]["reca"] + offset + (self["keytrj"]+1)*(_HISTORY_FORMAT[self["version"]]["recb"]+offset))*self["natms"]

        self._frameSize = self._configHeaderSize + self._configSize
        
        self['instance'].seek(0,2)

        self["n_frames"] = (self['instance'].tell()-self._headerSize)/self._frameSize
        
        self['instance'].seek(self._headerSize)

        data = self['instance'].read(self._configHeaderSize).splitlines()
              
        line = data[0].split()
              
        self._firstStep = int(line[1])

        self._timeStep = float(line[5])

        self._maskStep = 3+3*(self["keytrj"]+1)+1
        
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        if (self["version"] == u'3') or (self["version"] == u'4'):
            self._maskStep += 1
        
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        self['instance'].seek(0)        
                        
    def read_step(self, step):
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        self['instance'].seek(self._headerSize+step*self._frameSize)

        data = self['instance'].read(self._configHeaderSize).splitlines()
        
        line = data[0].split()
        
        currentStep = int(line[1])
        
        timeStep = (currentStep - self._firstStep)*self._timeStep
        
        cell = " ".join(data[1:]).split()

        cell = numpy.array(cell,dtype=numpy.float64)
        
        cell = numpy.reshape(cell,(3,3))*Units.Ang
                
        data = numpy.array(self['instance'].read(self._configSize).split())
        
        mask = numpy.ones((len(data),), dtype=numpy.bool)
        mask[0::self._maskStep] = False
        mask[1::self._maskStep] = False
        mask[2::self._maskStep] = False
        mask[3::self._maskStep] = False
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        if (self["version"] == u'3') or (self["version"] == u'4'):
            mask[4::self._maskStep] = False

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        config = numpy.array(numpy.compress(mask,data),dtype=numpy.float64)
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        config = numpy.reshape(config,(self["natms"],3*(self["keytrj"]+1)))
                
        config[:,0:3] *= Units.Ang
        
        if self["keytrj"] == 1:
            config[:,3:6] *= Units.Ang/Units.ps
            
        elif self["keytrj"] == 2:
            config[:,3:6] *= Units.Ang/Units.ps
            config[:,6:9] *= -Units.amu*Units.Ang/Units.ps**2

        return timeStep, cell, config
    
    def close(self):
        self["instance"].close()
                                           
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class DL_POLYConverter(Converter):
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    """
    Converts a DL_POLY trajectory to a MMTK trajectory.
    """
    
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    label = "DL-POLY"
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    settings = collections.OrderedDict()   
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    settings['field_file'] = ('input_file',{'wildcard':"FIELD files|FIELD*|All files|*",
                                            'default':os.path.join('..','..','..','Data','Trajectories','DL_Poly','FIELD_cumen')})
    settings['history_file'] = ('input_file',{'wildcard':"HISTORY files|HISTORY*|All files|*",
                                              'default':os.path.join('..','..','..','Data','Trajectories','DL_Poly','HISTORY_cumen')})
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    settings['atom_aliases'] = ('python_object',{'default':{}})
    settings['version'] = ('single_choice', {'choices':_HISTORY_FORMAT.keys(), 'default':'2'})
    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
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    def initialize(self):
        '''
        Initialize the job.
        '''
        
        self._atomicAliases = self.configuration["atom_aliases"]["value"]
        
        self._fieldFile = FieldFile(self.configuration["field_file"]["filename"], aliases=self._atomicAliases)
        
        self._historyFile = HistoryFile(self.configuration["history_file"]["filename"], self.configuration["version"]["value"])

        # The number of steps of the analysis.
        self.numberOfSteps = self._historyFile['n_frames']
                
        if self._historyFile["imcon"] == 0:
            self._universe = InfiniteUniverse()

        else:
            self._universe = ParallelepipedicPeriodicUniverse()
             
        self._fieldFile.build_mmtk_contents(self._universe)

        self._velocities = None
        
        self._forces = None

        if self._historyFile["keytrj"] == 1:
            self._universe.initializeVelocitiesToTemperature(0.)
            self._velocities = ParticleVector(self._universe)
            
        elif self._historyFile["keytrj"] == 2:
            self._universe.initializeVelocitiesToTemperature(0.)
            self._velocities = ParticleVector(self._universe)
            self._forces = ParticleVector(self._universe)
            
                        
        # A MMTK trajectory is opened for writing.
        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w', comment=self._fieldFile["title"])

        # A frame generator is created.
        self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])
        
    def run_step(self, index):
        """Runs a single step of the job.
        
        @param index: the index of the step.
        @type index: int.

        @note: the argument index is the index of the loop note the index of the frame.      
        """
                                                
        # The x, y and z values of the current frame.
        time, cell, config = self._historyFile.read_step(index)
        
        # If the universe is periodic set its shape with the current dimensions of the unit cell.
        if self._universe.is_periodic:
            self._universe.setShape(cell)
                    
        self._universe.setConfiguration(Configuration(self._universe, config[:,0:3]))
                   
        self._universe.foldCoordinatesIntoBox()
        
        data = {"time" : time}
        
        if self._velocities is not None:
            self._velocities.array = config[:,3:6]
            self._universe.setVelocities(self._velocities)

        if self._forces is not None:
            self._forces.array = config[:,6:9]
            data["forces"] = self._forces
                                        
        # Store a snapshot of the current configuration in the output trajectory.
        self._snapshot(data=data)
                                                                        
        return index, None
        
    def combine(self, index, x):
        """
        @param index: the index of the step.
        @type index: int.
        
        @param x:
        @type x: any.
        """
        
        pass
    
    def finalize(self):
        """
        Finalize the job.
        """
        
        self._historyFile.close()

        # Close the output trajectory.
        self._trajectory.close()
                
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REGISTRY['dl_poly'] = DL_POLYConverter