#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments #------------------------------------------------------------------------------------------ #Copyright (C) #2015- Eric C. Pellegrini Institut Laue-Langevin #BP 156 #71 avenue des Martyrs #38000 Grenoble Cedex 9 #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 :author: Eric C. Pellegrini ''' import collections import os import struct import numpy from MMTK import Units from MMTK.ParticleProperties import ParticleVector from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput from MDANSE.Externals.magnitude.magnitude import mg from MDANSE.Framework.Jobs.Converters.Converter import Converter from MDANSE.Framework.Jobs.Converters.MaterialsStudio import XTDFile FORCE_FACTOR = mg(1.0,"kcal_per_mole/ang","uma nm/ps2").toval() class TrjFile(dict): def __init__(self, trjfilename): self['instance'] = open(trjfilename, "rb") self.parse_header() def parse_header(self): trjfile = self['instance'] rec = "!4x" recSize = struct.calcsize(rec) trjfile.read(recSize) # Record 1 rec = "!4s20i8x" recSize = struct.calcsize(rec) DATA = struct.unpack(rec,trjfile.read(recSize)) VERSION = DATA[1] if VERSION < 2010: self._fp = "f" else: self._fp = "d" # Diff with doc --> NTRJTI and TRJTIC not in doc rec = '!i' recSize = struct.calcsize(rec) NTRJTI, = struct.unpack(rec, trjfile.read(recSize)) rec = '!%ds8x' % (80*NTRJTI) recSize = struct.calcsize(rec) self["title"] = struct.unpack(rec, trjfile.read(recSize)) self["title"] = "".join(self["title"]) # Record 2 rec = "!i" recSize = struct.calcsize(rec) NEEXTI = struct.unpack(rec,trjfile.read(recSize))[0] rec = "!" + "%ds" % (80*NEEXTI) + '8x' recSize = struct.calcsize(rec) trjfile.read(recSize) # Record 3 rec = "!8i8x" recSize = struct.calcsize(rec) PERTYPE,_,LCANON,DEFCEL,_,_,LNPECAN,LTMPDAMP = struct.unpack(rec,trjfile.read(recSize)) self["pertype"] = PERTYPE self["defcel"] = DEFCEL # Record 4 rec = "!i" recSize = struct.calcsize(rec) NFLUSD = struct.unpack(rec,trjfile.read(recSize))[0] rec = '!%di%di%ds8x' % (NFLUSD,NFLUSD,8*NFLUSD) recSize = struct.calcsize(rec) trjfile.read(recSize) rec = '!i' recSize = struct.calcsize(rec) self["totmov"] = struct.unpack(rec,trjfile.read(recSize))[0] rec = '!%di8x' % self["totmov"] recSize = struct.calcsize(rec) self["mvofst"] = numpy.array(struct.unpack(rec,trjfile.read(recSize)), dtype=numpy.int32) - 1 # Record 4a rec = "!i" recSize = struct.calcsize(rec) LEEXTI, = struct.unpack(rec,trjfile.read(recSize)) rec = "!%ds8x" % LEEXTI recSize = struct.calcsize(rec) trjfile.read(recSize) # Record 4b rec = "!i" recSize = struct.calcsize(rec) LPARTI, = struct.unpack(rec,trjfile.read(recSize)) rec = "!%ds8x" % LPARTI recSize = struct.calcsize(rec) trjfile.read(recSize) self._headerSize = trjfile.tell() # Frame record 1 if VERSION == 2000: rec1 = '!%si33%s5i8x' % (self._fp,self._fp) elif VERSION == 2010: rec1 = '!%si57%s6i8x' % (self._fp,self._fp) else: rec1 = '!%si58%s6i8x' % (self._fp,self._fp) recSize = struct.calcsize(rec1) DATA = struct.unpack(rec1,trjfile.read(recSize)) if VERSION < 2010: self["velocities_written"] = DATA[-3] self["forces_written"] = 0 else: self["velocities_written"] = DATA[-4] self["forces_written"] = DATA[-3] # Frame record 2 rec = '!12%s8x' % self._fp recSize = struct.calcsize(rec) trjfile.read(recSize) # Frame record 3 if LCANON: rec = '!4%s8x' % self._fp recSize = struct.calcsize(rec) trjfile.read(recSize) if PERTYPE > 0: # Frame record 4 self._defCellRecPos = trjfile.tell() - self._headerSize self._defCellRec = '!22%s8x' % self._fp self._defCellRecSize = struct.calcsize(self._defCellRec) trjfile.read(self._defCellRecSize) if PERTYPE > 0: # Frame record 5 rec = '!i14%s8x' % self._fp recSize = struct.calcsize(rec) trjfile.read(recSize) if LNPECAN: # Frame record 6 rec = '!3%s8x' % self._fp recSize = struct.calcsize(rec) trjfile.read(recSize) if LTMPDAMP: # Frame record 7 rec = '!%s8x' % self._fp recSize = struct.calcsize(rec) trjfile.read(recSize) self._configRecPos = trjfile.tell() - self._headerSize if self["velocities_written"]: if self["forces_written"]: # Frame record 8,9,10,11,12,13,14,15,16 self._configRec = '!' + ('%d%s8x'*9) % ((self['totmov'],self._fp)*9) else: # Frame record 8,9,10,11,12,13 self._configRec = '!' + ('%d%s8x'*6) % ((self['totmov'],self._fp)*6) else: if self["forces_written"]: # Frame record 8,9,10,14,15,16 self._configRec = '!' + ('%d%s8x'*6) % ((self['totmov'],self._fp)*6) else: # Frame record 8,9,10 self._configRec = '!' + ('%d%s8x'*3) % ((self['totmov'],self._fp)*3) self._configRecSize = struct.calcsize(self._configRec) trjfile.read(self._configRecSize) self._frameSize = trjfile.tell() - self._headerSize trjfile.seek(0,2) self["n_frames"] = (trjfile.tell()-self._headerSize)/self._frameSize def read_step(self, index): """ """ trjfile = self["instance"] pos = self._headerSize + index*self._frameSize trjfile.seek(pos,0) rec = '!%s' % self._fp recSize = struct.calcsize(rec) timeStep, = struct.unpack(rec,trjfile.read(recSize)) if self["defcel"]: trjfile.seek(pos + self._defCellRecPos,0) cell = numpy.zeros((3,3),dtype=numpy.float64) # ax,by,cz,bz,az,ay cellData = numpy.array(struct.unpack(self._defCellRec,trjfile.read(self._defCellRecSize)),dtype=numpy.float64)[2:8]*Units.Ang cell[0,0] = cellData[0] cell[1,1] = cellData[1] cell[2,2] = cellData[2] cell[1,2] = cellData[3] cell[0,2] = cellData[4] cell[0,1] = cellData[5] else: cell = None trjfile.seek(pos + self._configRecPos,0) config = struct.unpack(self._configRec,trjfile.read(self._configRecSize)) if self["velocities_written"]: if self["forces_written"]: config = numpy.transpose(numpy.reshape(config,(3,3, self['totmov']))) xyz = config[:,:,0]*Units.Ang vel = config[:,:,1]*Units.Ang forces = config[:,:,2]*FORCE_FACTOR else: config = numpy.transpose(numpy.reshape(config,(2,3, self['totmov']))) xyz = config[:,:,0]*Units.Ang vel = config[:,:,1]*Units.Ang forces = None else: if self["forces_written"]: config = numpy.transpose(numpy.reshape(config,(2,3, self['totmov']))) xyz = config[:,:,0]*Units.Ang vel = None forces = config[:,:,1]*FORCE_FACTOR else: config = numpy.transpose(numpy.reshape(config,(1,3, self['totmov']))) xyz = config[:,:,0]*Units.Ang vel = None forces = None return timeStep, cell, xyz, vel, forces def close(self): self["instance"].close() class ForciteConverter(Converter): """ Converts a Forcite trajectory to a MMTK trajectory. """ type = 'forcite' label = "Forcite" category = ('Converters','Materials Studio') ancestor = None settings = collections.OrderedDict() settings['xtd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Forcite','nylon66_rho100_500K_v300K.xtd')}) settings['trj_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Forcite','nylon66_rho100_500K_v300K.trj')}) settings['output_file'] = ('output_files', {'formats':["netcdf"]}) def initialize(self): ''' Initialize the job. ''' self._xtdfile = XTDFile(self.configuration["xtd_file"]["filename"]) self._xtdfile.build_universe() self._universe = self._xtdfile.universe self._trjfile = TrjFile(self.configuration["trj_file"]["filename"]) # The number of steps of the analysis. self.numberOfSteps = self._trjfile['n_frames'] self._velocities = None self._forces = None if self._trjfile["velocities_written"]: self._velocities = ParticleVector(self._universe) self._velocities.array[:,:] = 0.00 if self._trjfile["forces_written"]: self._forces = ParticleVector(self._universe) self._forces.array[:,:] = 0.00 # A MMTK trajectory is opened for writing. self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w', comment=self._trjfile["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, xyz, vel, forces = self._trjfile.read_step(index) # If the universe is periodic set its shape with the current dimensions of the unit cell. if self._universe.is_periodic and self._trjfile["defcel"]: self._universe.setShape(cell) movableAtoms = self._trjfile['mvofst'] self._universe.configuration().array[movableAtoms,:] = xyz self._universe.foldCoordinatesIntoBox() data = {"time" : time} if self._velocities is not None: self._velocities.array[movableAtoms,:] = vel self._universe.setVelocities(self._velocities) if self._forces is not None: self._forces.array[movableAtoms,:] = forces 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._trjfile.close() # Close the output trajectory. self._trajectory.close()