Révision 15 ase/embed.py
| embed.py (revision 15) | ||
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| 16 | 16 |
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class Embed(Atoms): |
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#--- constructor of the Embed class --- |
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def __init__(self, system=None, cluster=None, cell_cluster = "Auto"):
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def __init__(self, system, cluster, cell_cluster = "Auto", cluster_pos = True):
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super(Embed, self).__init__() |
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# define the atom map |
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self.atom_map_sys_cl = [] |
| ... | ... | |
| 28 | 28 |
# set the search radius for link atoms |
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self.d = 10 |
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# define the systems for calculations |
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if system is None or cluster is None: |
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raise RuntimeError("Embed: system or cluster is not definied")
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self.set_system(system) |
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self.set_cluster(cluster) |
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if cluster_pos: |
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self.set_cluster(cluster) |
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else: |
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self.set_cluster_by_numbers(cluster) |
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# set the cell of the system |
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self.set_cell(system.get_cell()) |
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self.cell_cluster = cell_cluster |
| ... | ... | |
| 58 | 64 |
# set the cluster for low and high level calculation |
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self.atoms_cluster = atoms |
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return |
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#--- set cluster by atom numbers --- |
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def set_cluster_by_numbers(self, numbers): |
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cluster = Atoms() |
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nat = len(self.atoms_system) |
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for number in numbers: |
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if nat > numbers: |
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raise RuntimeError("QMX: The number of the cluster atom ", number, "is bigger than the number of atoms")
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cluster.append(self.atoms_system[number-1]) |
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self.set_cluster(cluster) |
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#--- set the system --- |
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def set_system(self, atoms): |
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