DensityOfStates.py 8.15 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
#------------------------------------------------------------------------------------------
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#6, rue Jules Horowitz
#38042 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: pellegrini
'''

import collections

from MDANSE import ELEMENTS
from MDANSE.Framework.Jobs.IJob import IJob
from MDANSE.Mathematics.Arithmetic import weight
38
from MDANSE.Mathematics.Signal import correlation, differentiate, get_spectrum
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
from MDANSE.MolecularDynamics.Trajectory import read_atoms_trajectory

class DensityOfStates(IJob):
    """
    The Density Of States correspond, for a set of atoms, to the calculation of the 
    power spectrum of the Velocity AutoCorrelation Function (VACF), which in case of 
    the mass-weighted VACF defines the phonon discrete Density Of States.
    """

    type = 'dos'
    
    label = "Density Of States"

    category = ('Dynamics',)
    
    ancestor = "mmtk_trajectory"

56
57
58
59
    settings = collections.OrderedDict()
    settings['trajectory'] = ('mmtk_trajectory',{})
    settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}})
    settings['instrument_resolution'] = ('instrument_resolution',{'dependencies':{'trajectory':'trajectory',
60
                                                                                       'frames' : 'frames'}})
61
    settings['interpolation_order'] = ('interpolation_order', {'label':"velocities",
62
                                                                    'dependencies':{'trajectory':'trajectory'}})
63
64
    settings['projection'] = ('projection', {'label':"project coordinates"})
    settings['atom_selection'] = ('atom_selection',{'dependencies':{'trajectory':'trajectory',
65
                                                                         'grouping_level':'grouping_level'}})
66
67
    settings['grouping_level'] = ('grouping_level',{})
    settings['atom_transmutation'] = ('atom_transmutation',{'dependencies':{'trajectory':'trajectory',
68
                                                                                 'atom_selection':'atom_selection'}})        
69
70
71
    settings['weights'] = ('weights',{})
    settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]})
    settings['running_mode'] = ('running_mode',{})
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
    
    def initialize(self):
        """
        Initialize the input parameters and analysis self variables
        """

        self.numberOfSteps = self.configuration['atom_selection']['n_groups']

        instrResolution = self.configuration["instrument_resolution"]        
                
        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
        self._outputData.add("time_window","line", instrResolution["time_window"], axis="time", units="au") 

        self._outputData.add("frequency","line", instrResolution["frequencies"], units='THz')
        self._outputData.add("frequency_window","line", instrResolution["frequency_window"], axis="frequency", units="au") 
            
        for element in self.configuration['atom_selection']['contents'].keys():
            self._outputData.add("vacf_%s" % element,"line", (self.configuration['frames']['number'],), axis="time", units="nm2/ps2") 
            self._outputData.add("dos_%s" % element,"line", (instrResolution['n_frequencies'],), axis="frequency", units="nm2/ps") 
        self._outputData.add("vacf_total","line", (self.configuration['frames']['number'],), axis="time", units="nm2/ps2")         
        self._outputData.add("dos_total","line", (instrResolution['n_frequencies'],), axis="frequency", units="nm2/ps")        
        
    def run_step(self, index):
        """
        Runs a single step of the job.\n
 
        :Parameters:
            #. index (int): The index of the step.
        :Returns:
            #. index (int): The index of the step. 
            #. atomicDOS (numpy.array): The calculated density of state for atom of index=index
            #. atomicVACF (numpy.array): The calculated velocity auto-correlation function for atom of index=index
        """

        # get atom index
        indexes = self.configuration['atom_selection']["groups"][index]    
                        
        series = read_atoms_trajectory(self.configuration["trajectory"]["instance"],
                                       indexes,
                                       first=self.configuration['frames']['first'],
                                       last=self.configuration['frames']['last']+1,
                                       step=self.configuration['frames']['step'],
                                       variable=self.configuration['interpolation_order']["variable"])

116
117
118
        val = self.configuration["interpolation_order"]["value"]
        
        if val != "no interpolation":     
119
            for axis in range(3):
120
                series[:,axis] = differentiate(series[:,axis], order=val, dt=self.configuration['frames']['time_step'])
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171

        if self.configuration["projection"]["projector"] is not None:
            series = self.configuration['projection']["projector"](series)
            
        atomicVACF = correlation(series,axis=0,reduce=1)

        return index, atomicVACF

    def combine(self, index, x):
        """
        Combines returned results of run_step.\n
        :Parameters:
            #. index (int): The index of the step.\n
            #. x (any): The returned result(s) of run_step
        """   

        # The symbol of the atom.
        element = self.configuration['atom_selection']['elements'][index][0]
        
        self._outputData["vacf_%s" % element] += x
                
    def finalize(self):
        """
        Finalizes the calculations (e.g. averaging the total term, output files creations ...).
        """
        
        for element, number in self.configuration['atom_selection']['n_atoms_per_element'].items():
            self._outputData["vacf_%s" % element][:] /= number
            self._outputData["dos_%s" % element][:] = get_spectrum(self._outputData["vacf_%s" % element],
                                                                   self.configuration["instrument_resolution"]["time_window"],
                                                                   self.configuration["instrument_resolution"]["time_step"])

        props = dict([[k,ELEMENTS[k,self.configuration["weights"]["property"]]] for k in self.configuration['atom_selection']['n_atoms_per_element'].keys()])
        
        vacfTotal = weight(props,
                           self._outputData,
                           self.configuration['atom_selection']['n_atoms_per_element'],
                           1,
                           "vacf_%s")
        self._outputData["vacf_total"][:] = vacfTotal
        
        dosTotal = weight(props,
                          self._outputData,
                          self.configuration['atom_selection']['n_atoms_per_element'],
                          1,
                          "dos_%s")
        self._outputData["dos_total"][:] = dosTotal        
        
        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
        
        self.configuration['trajectory']['instance'].close()