Ejemplo n.º 1
0
 def init_first(self):
     AnalysisHook.init_first(self)
     if self.outg is not None:
         self.outg.create_dataset('amps', (self.ssize,), float)
         self.outg.create_dataset('freqs', (self.ssize,), float)
         self.outg.create_dataset('ac', (self.ssize,), float)
         self.outg.create_dataset('time', (self.ssize,), float)
Ejemplo n.º 2
0
 def init_first(self):
     # update the shape if select is present
     if self.select is not None:
         self.shape = (len(self.select), ) + self.shape[1:]
     # compute the number of dimensions, i.e. 3 for atoms
     self.ndim = 1
     for s in self.shape[1:]:
         self.ndim *= s
     # allocate working arrays
     self.last_poss = [
         np.zeros(self.shape, float) for i in range(self.mult)
     ]
     self.pos = np.zeros(self.shape, float)
     # prepare the hdf5 output file, if present.
     AnalysisHook.init_first(self)
     if self.outg is not None:
         for m in range(self.mult):
             self.outg.create_dataset('msd%03i' % (m + 1),
                                      shape=(0, ),
                                      maxshape=(None, ),
                                      dtype=float)
         self.outg.create_dataset('msdsums', data=self.msdsums)
         self.outg.create_dataset('msdcounters', data=self.msdcounters)
         self.outg.create_dataset('pars', shape=(2, ), dtype=float)
         self.outg.create_dataset('pars_error', shape=(2, ), dtype=float)
Ejemplo n.º 3
0
Archivo: rdf.py Proyecto: mcoolsce/yaff
 def init_first(self):
     '''Setup some work arrays'''
     # determine the number of atoms
     if self.select0 is None:
         self.natom0 = self.natom
     else:
         self.natom0 = len(self.select0)
     self.pos0 = np.zeros((self.natom0, 3), float)
     # the number of pairs
     if self.select1 is None:
         self.npair = (self.natom0 * (self.natom0 - 1)) // 2
         self.pos1 = None
     else:
         self.natom1 = len(self.select1)
         self.pos1 = np.zeros((self.natom1, 3), float)
         self.npair = self.natom0 * self.natom1
     # multiply the number of pairs by all images
     self.npair *= (1 + 2 * self.nimage)**3
     # Prepare the output
     self.work = np.zeros(self.npair, float)
     AnalysisHook.init_first(self)
     if self.outg is not None:
         self.outg.create_dataset('rdf', (self.nbin, ), float)
         self.outg.create_dataset('CN', (self.nbin, ), float)
         self.outg['d'] = self.d
         if self.pairs_sr is not None:
             self.outg.create_dataset('rdf_sr', (self.nbin, ), float)
Ejemplo n.º 4
0
 def init_first(self):
     AnalysisHook.init_first(self)
     if self.outg is not None:
         self.outg.create_dataset("amps", (self.ssize,), float)
         self.outg.create_dataset("freqs", (self.ssize,), float)
         self.outg.create_dataset("ac", (self.ssize,), float)
         self.outg.create_dataset("time", (self.ssize,), float)
Ejemplo n.º 5
0
 def init_first(self):
     AnalysisHook.init_first(self)
     if self.outg is not None:
         self.outg.create_dataset('amps', (self.ssize, ), float)
         self.outg.create_dataset('freqs', (self.ssize, ), float)
         self.outg.create_dataset('ac', (self.ssize, ), float)
         self.outg.create_dataset('time', (self.ssize, ), float)
Ejemplo n.º 6
0
Archivo: rdf.py Proyecto: tovrstra/yaff
 def init_first(self):
     '''Setup some work arrays'''
     # determine the number of atoms
     if self.select0 is None:
         self.natom0 = self.natom
     else:
         self.natom0 = len(self.select0)
     self.pos0 = np.zeros((self.natom0, 3), float)
     # the number of pairs
     if self.select1 is None:
         self.npair = (self.natom0*(self.natom0-1))/2
         self.pos1 = None
     else:
         self.natom1 = len(self.select1)
         self.pos1 = np.zeros((self.natom1, 3), float)
         self.npair = self.natom0*self.natom1
     # multiply the number of pairs by all images
     self.npair *= (1 + 2*self.nimage)**3
     # Prepare the output
     self.work = np.zeros(self.npair, float)
     AnalysisHook.init_first(self)
     if self.outg is not None:
         self.outg.create_dataset('rdf', (self.nbin,), float)
         self.outg['d'] = self.d
         if self.pairs_sr is not None:
             self.outg.create_dataset('rdf_sr', (self.nbin,), float)
Ejemplo n.º 7
0
 def init_first(self):
     # update the shape if select is present
     if self.select is not None:
         self.shape = (len(self.select),) + self.shape[1:]
     # compute the number of dimensions, i.e. 3 for atoms
     self.ndim = 1
     for s in self.shape[1:]:
         self.ndim *= s
     # allocate working arrays
     self.last_poss = [np.zeros(self.shape, float) for i in range(self.mult)]
     self.pos = np.zeros(self.shape, float)
     # prepare the hdf5 output file, if present.
     AnalysisHook.init_first(self)
     if self.outg is not None:
         for m in range(self.mult):
             self.outg.create_dataset('msd%03i' % (m+1), shape=(0,), maxshape=(None,), dtype=float)
         self.outg.create_dataset('msdsums', data=self.msdsums)
         self.outg.create_dataset('msdcounters', data=self.msdcounters)
         self.outg.create_dataset('pars', shape=(2,), dtype=float)
         self.outg.create_dataset('pars_error', shape=(2,), dtype=float)