Révision 17 ase/embed.py

embed.py (revision 17)
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            self.atoms_cluster.set_cell(self.atoms_system.get_cell())
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        elif self.cell_cluster == "Auto":
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            positions = self.atoms_cluster.get_positions()
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            #find the biggest dimensions of the cluster in x,y,z direction
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            l = 0
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            for idir in xrange(3):
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                l = max(l, positions[:, idir].max() - positions[:, idir].min())
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            # calculate the box parameters (cluster + min 5 Ang)
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            l = (math.floor(l/2.5)+1)*2.5 + 5.0
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            # build cell
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            cell = np.zeros((3, 3),  float)
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            # apply cell parameters
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            #for all directions
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            for idir in xrange(3):
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                #find the biggest dimensions of the cluster in x,y,z direction
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                l = positions[:, idir].max() - positions[:, idir].min()
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                # calculate the box parameters (2*cluster + 60 pm)
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                l = (math.floor((2*l+6)/2.5)+1)*2.5
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                # apply cell parameters
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                cell[idir, idir] = l
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            # set parameters to cluster
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            self.atoms_cluster.set_cell(cell)
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            # print information on the screen
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            print "length of box surrounding the cluster: ",
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            print l*10,
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            print "pm"
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            print "dimension of box surrounding the cluster: ",
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            for idir in xrange(3):
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                print cell[idir, idir]*10,
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            print " pm"
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            exit()
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        else:
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            self.atoms_cluster.set_cell(self.cell_cluster)
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