AngularAutoCorrelationsTwoAxes.py

# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
#   NScD Oak Ridge National Laboratory, European Spallation Source,
#   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=too-many-branches,too-many-locals, invalid-name
from mantid.simpleapi import *
from mantid.kernel import *
from mantid.api import *

from scipy.io import netcdf
import numpy as np
import re
import time


class AngularAutoCorrelationsTwoAxes(PythonAlgorithm):

    def category(self):
        return "Simulation"

    def summary(self):
        return ("Calculates the angular auto-correlations of molecules in a simulation along two user-defined axes. "
                "The first axis is defined by the vector connecting the average position of species two and the average position "
                "of species one (user input). The second axis is perpendicular to axis 1 and is constructed by considering one "
                "arbitrary atom of species 3 (user input). Timestep must be specified in femtoseconds.")

    def PyInit(self):
        self.declareProperty(FileProperty('InputFile','',action=FileAction.Load),doc="Input .nc file with an MMTK trajectory")

        self.declareProperty("Timestep", "1.0", direction=Direction.Input,
                             doc="Time step between two coordinates in the trajectory in femtoseconds")

        self.declareProperty("SpeciesOne",'',direction=Direction.Input,doc="Specify the first species, e.g. H, He, Li...")
        self.declareProperty("SpeciesTwo",'',direction=Direction.Input,doc="Specify the second species, e.g. H, He, Li...")
        self.declareProperty("SpeciesThree",'',direction=Direction.Input,doc="Specify the third species, e.g. H, He, Li...")

        self.declareProperty(WorkspaceProperty('OutputWorkspace','',direction=Direction.Output),doc="Output workspace name")
        self.declareProperty(WorkspaceProperty('OutputWorkspaceFT','FT',direction=Direction.Output),doc="FT Output workspace name")

    def PyExec(self):
        # Get file path
        file_name=self.getPropertyValue("InputFile")

        # Get the user-specified species
        types=[self.getPropertyValue("SpeciesOne").lower(),
               self.getPropertyValue("SpeciesTwo").lower(),
               self.getPropertyValue("SpeciesThree").lower()]

        # Load trajectory file
        trajectory=netcdf.netcdf_file(file_name,mode="r")

        logger.information("Loading particle id's, molecule id's and coordinate array...")
        start_time=time.time()

        # netcdf object containing the particle id numbers
        description=(trajectory.variables["description"])[:]

        # Convert description object to string via for loop. The original object has strange formatting
        particleID = ''
        for i in description:
            particleID += i.decode('UTF-8')

        # Extract particle id's from string using regular expressions
        p_atoms=re.findall(r"A\('[a-z]+\d+',\d+", particleID)

        # Split the string s by molecules
        molecules=particleID.split("AC")

        # Remove first item of molecule list (contains initialisation of variable 'description')
        del molecules[0]

        # Many-to-one structures. Identify the set of atomic species present (list structure 'elements')
        # in the simulation and repackage particles into a dictionary 'particles_to_species' with structure id number -> species
        atoms_to_species={}
        species_to_atoms={}
        elements=[]

        # Populate the particles_to_species dictionary and the elements list
        for j in p_atoms:
            key=re.findall(r"',\d+",j)[0]
            key=int(re.findall(r"\d+",key)[0])
            element=re.findall(r"[a-z]+",j)[0]
            if element not in elements:
                elements.append(str(element))
            atoms_to_species[key]=str(element)

        # Check wether user-specified species present in the trajectory file
        for i in range(3):
            if types[i] not in elements:
                raise RuntimeError('Species '+['one','two','three'][i]+' not found in the trajectory file. Please try again...')

        # Initialise lists in the species_to_particles dictionary
        for j in elements:
            species_to_atoms[j]=[]

        # Populate the species_to_particles dictionary
        for j in p_atoms:
            key=re.findall(r"',\d+",j)[0]
            key=int(re.findall(r"\d+",key)[0])
            element=re.findall(r"[a-z]+",j)[0]
            species_to_atoms[element].append(key)

        # Many-to-one structures. Assign atom indices to molecule indices using a dictionaries
        # with structures atom id -> molecule id and molecule id -> list of atoms ids
        atoms_to_molecules={}
        molecules_to_atoms={}

        # Initialise lists in the molecule_to_atom dictionary
        for k in range(len(molecules)):
            molecules_to_atoms[k]=[]

        # Populate the dictionaries with atoms & molecules
        for k in range(len(molecules)):
            r_atoms=re.findall(r"A\('[a-z]+\d+',\d+",molecules[k])
            for i in r_atoms:
                key=re.findall(r"',\d+",i)[0]
                key=int(re.findall(r"\d+",key)[0])
                atoms_to_molecules[key]=k
                molecules_to_atoms[k].append(key)

        # Coordinate array. Shape: timesteps x (# of particles) x (# of spatial dimensions)
        configuration=trajectory.variables["configuration"]

        # Extract useful simulation parameters
        # Number of species present in the simulation
        # n_species=len(elements)
        # Number of particles present in the simulation
        n_particles=len(p_atoms)
        # Number of molecules present in the simulation
        n_molecules=len(molecules)
        # Number of timesteps in the simulation
        n_timesteps=int(configuration.shape[0])
        # Number of spatial dimensions
        n_dimensions=int(configuration.shape[2])

        logger.information(str(time.time()-start_time) + " s")

        logger.information("Transforming coordinates...")
        start_time=time.time()

        # Box size for each timestep. Shape: timesteps x (3 consecutive 3-vectors)
        box_size=trajectory.variables["box_size"]

        # Reshape the paralellepipeds into 3x3 tensors for coordinate transformations.
        # Shape: (# of timesteps) x (3-vectors) x (# of spatial dimensions)
        box_size_tensors=10.0*np.array([box_size[j].reshape((3,3)) for j in range(n_timesteps)])

        # Extract box dimensions (assuming orthorhombic simulation cell, diagonal matrix)
        box_size_x=np.array([box_size_tensors[i,0,0] for i in range(n_timesteps)])
        box_size_y=np.array([box_size_tensors[i,1,1] for i in range(n_timesteps)])
        box_size_z=np.array([box_size_tensors[i,2,2] for i in range(n_timesteps)])

        # Copy the configuration object into a numpy array
        configuration_copy=np.array([configuration[i] for i in range(n_timesteps)])

        # Swap the time and particle axes
        configuration_copy=np.swapaxes(configuration_copy,0,1)

        # Transform particle trajectories (configuration array) to Cartesian coordinates at each time step.
        cartesian_configuration=np.array([[np.dot(box_size_tensors[j],np.transpose(configuration_copy[i,j]))
                                           for j in range(n_timesteps)] for i in range(n_particles)])

        logger.information(str(time.time()-start_time) + " s")

        logger.information("Calculating orientation vectors...")
        start_time=time.time()

        # Initialise orientation vector array. Shape: (# of molecules) x (# of timesteps) x (# of dimensions)
        orientation_vectors1=np.zeros((n_molecules,n_timesteps,n_dimensions))
        orientation_vectors2=np.zeros((n_molecules,n_timesteps,n_dimensions))

        for i in range(n_molecules):
            # Retrieve constituents of the ith molecule
            temp=molecules_to_atoms[i]
            # Find which constituents belong to species one, species two and species three
            species_one=[]
            species_two=[]
            species_three=[]
            for j in temp:
                if atoms_to_species[j]==types[0]:
                    species_one.append(j)
                if atoms_to_species[j]==types[1]:
                    species_two.append(j)
                if atoms_to_species[j]==types[2]:
                    species_three.append(j)
            # Find the average positions of species one and two
            sum_position_species_one=np.zeros((n_timesteps,n_dimensions))
            sum_position_species_two=np.zeros((n_timesteps,n_dimensions))
            for k in species_one:
                sum_position_species_one+=cartesian_configuration[k]
            for l in species_two:
                sum_position_species_two+=cartesian_configuration[l]
            avg_position_species_one=1.0*sum_position_species_one/float(len(species_one))
            avg_position_species_two=1.0*sum_position_species_two/float(len(species_two))
            # Choose the 1st element of species_three to build the 2nd vector
            position_species_three=1.0*cartesian_configuration[species_three[0]]

            # Find the vectors connecting average positions of species one and species two
            vectors1=avg_position_species_two-avg_position_species_one

            # Find the vector to the third atom
            vectors2=position_species_three-avg_position_species_two

            diffX1=np.divide(vectors1[:,0],box_size_x)
            diffY1=np.divide(vectors1[:,1],box_size_y)
            diffZ1=np.divide(vectors1[:,2],box_size_z)

            diffX2=np.divide(vectors2[:,0],box_size_x)
            diffY2=np.divide(vectors2[:,1],box_size_y)
            diffZ2=np.divide(vectors2[:,2],box_size_z)

            # Wrapping the vectors
            vectorX1=np.array([(diffX1[k]-round(diffX1[k]))*box_size_x[k] for k in range(n_timesteps)])
            vectorY1=np.array([(diffY1[k]-round(diffY1[k]))*box_size_y[k] for k in range(n_timesteps)])
            vectorZ1=np.array([(diffZ1[k]-round(diffZ1[k]))*box_size_z[k] for k in range(n_timesteps)])

            vectorX2=np.array([(diffX2[k]-round(diffX2[k]))*box_size_x[k] for k in range(n_timesteps)])
            vectorY2=np.array([(diffY2[k]-round(diffY2[k]))*box_size_y[k] for k in range(n_timesteps)])
            vectorZ2=np.array([(diffZ2[k]-round(diffZ2[k]))*box_size_z[k] for k in range(n_timesteps)])

            # Normalisation
            norm1=np.sqrt(vectorX1*vectorX1+vectorY1*vectorY1+vectorZ1*vectorZ1)
            vectorX1=np.divide(vectorX1,norm1)
            vectorY1=np.divide(vectorY1,norm1)
            vectorZ1=np.divide(vectorZ1,norm1)

            norm2=np.sqrt(vectorX2*vectorX2+vectorY2*vectorY2+vectorZ2*vectorZ2)
            vectorX2=np.divide(vectorX2,norm2)
            vectorY2=np.divide(vectorY2,norm2)
            vectorZ2=np.divide(vectorZ2,norm2)

            # Dot product
            cosine=np.multiply(vectorX1,vectorX2)+np.multiply(vectorY1,vectorY2)+np.multiply(vectorZ1,vectorZ2)

            # Gram-Schmidt orthogonalisation process
            vectorX2=vectorX2-np.divide(vectorX1,cosine)
            vectorY2=vectorY2-np.divide(vectorY1,cosine)
            vectorZ2=vectorZ2-np.divide(vectorZ1,cosine)

            # Renormalisation of the 2nd vector
            norm2=np.sqrt(vectorX2*vectorX2+vectorY2*vectorY2+vectorZ2*vectorZ2)
            vectorX2=np.divide(vectorX2,norm2)
            vectorY2=np.divide(vectorY2,norm2)
            vectorZ2=np.divide(vectorZ2,norm2)

            # Store calculations in the orientation_vectors1 and orientation_vectors2 arrays
            orientation_vectors1[i]=np.swapaxes(np.array([vectorX1,vectorY1,vectorZ1]),0,1)
            orientation_vectors2[i]=np.swapaxes(np.array([vectorX2,vectorY2,vectorZ2]),0,1)

        logger.information(str(time.time()-start_time) + " s")

        logger.information("Calculating angular auto-correlations...")
        start_time=time.time()

        # First axis
        R_avg_axis1=np.zeros(n_timesteps)
        for i in range(n_molecules):
            R_avg_axis1+=self.auto_correlation(orientation_vectors1[i])

        R_avg_axis1=1.0*R_avg_axis1/n_molecules

        # Second axis
        R_avg_axis2=np.zeros(n_timesteps)
        for i in range(n_molecules):
            R_avg_axis2+=self.auto_correlation(orientation_vectors2[i])

        R_avg_axis2=1.0*R_avg_axis2/n_molecules

        logger.information(str(time.time()-start_time)+" s")

        # Initialise & populate the output_ws workspace
        nrows=2
        step=float(self.getPropertyValue("Timestep"))
        xvals=np.arange(0,np.ceil((n_timesteps)/2.0))*step/1000.0
        yvals=np.empty(0)
        yvals=np.append(yvals,self.fold_correlation(R_avg_axis1))
        yvals=np.append(yvals,self.fold_correlation(R_avg_axis2))
        evals=np.zeros(np.shape(yvals))

        output_name=self.getPropertyValue("OutputWorkspace")
        output_ws=CreateWorkspace(OutputWorkspace=output_name,DataX=xvals,UnitX="ps",DataY=yvals,
                                  DataE=evals,NSpec=nrows,VerticalAxisUnit="Text",VerticalAxisValues=["Axis 1","Axis 2"])
        # Set output workspace to output_ws
        self.setProperty('OutputWorkspace',output_ws)

        # Fourier transform output to workspace
        nrows=2
        yvals=np.empty(0)
        yvals=np.append(yvals,np.fft.rfft(R_avg_axis1))
        yvals=np.append(yvals,np.fft.rfft(R_avg_axis2))
        evals=np.zeros(np.shape(yvals))
        xvals=np.arange(0,np.shape(yvals)[0])

        FT_output_name=self.getPropertyValue("OutputWorkspaceFT")
        FT_output_ws=CreateWorkspace(OutputWorkspace=FT_output_name,DataX=xvals,UnitX="1/fs",DataY=yvals,
                                     DataE=evals,NSpec=nrows,VerticalAxisUnit="Text",VerticalAxisValues=["FT Axis 1","FT Axis 2"])
        self.setProperty("OutputWorkspaceFT",FT_output_ws)

    def auto_correlation(self, vector):
        # Returns angular auto-correlation of a normalised time-dependent 3-vector
        num=np.shape(vector)[0]
        norm=np.arange(np.ceil(num/2.0),num+1)
        norm=np.append(norm,(np.arange(int(num/2)+1,num)[::-1]))

        # x dimension
        autoCorr=np.divide(np.correlate(vector[:,0],vector[:,0],"same"),norm)
        # y dimension
        autoCorr+=np.divide(np.correlate(vector[:,1],vector[:,1],"same"),norm)
        # z dimension
        autoCorr+=np.divide(np.correlate(vector[:,2],vector[:,2],"same"),norm)

        return autoCorr

    def fold_correlation(self,omega):
        # Folds an array with symmetrical values into half by averaging values around the centre
        right_half=omega[int(len(omega))//2:]
        left_half=omega[:int(np.ceil(len(omega)/2.0))][::-1]

        return (left_half+right_half)/2.0


# Subscribe algorithm to Mantid software
AlgorithmFactory.subscribe(AngularAutoCorrelationsTwoAxes)