Exemple #1
0
    def setup(self):
        files = os.listdir(".")
        num_structures = 0
        if not set(files).issuperset(VASP_INPUT_FILES):
            for f in files:
                try:
                    struct = read_structure(f)
                    num_structures += 1
                except:
                    pass
            if num_structures != 1:
                raise RuntimeError("{} structures found. Unable to continue."
                                   .format(num_structures))
            else:
                self.default_vis.write_input(struct, ".")

        if self.backup:
            for f in VASP_INPUT_FILES:
                shutil.copy(f, "{}.orig".format(f))

        if self.auto_npar:
            try:
                vi = VaspInput.from_directory(".")
                incar = vi["INCAR"]
                #Only optimized NPAR for non-HF and non-RPA calculations.
                if (not incar.get("LHFCALC")) and (not incar.get("LRPA")):
                    import multiprocessing
                    ncores = multiprocessing.cpu_count()
                    for npar in range(int(round(math.sqrt(ncores))), ncores):
                        if ncores % npar == 0:
                            incar["NPAR"] = npar
                            break
                    incar.write_file("INCAR")
            except:
                pass

        if self.settings_override is not None:
            vi = VaspInput.from_directory(".")
            m = Modder([FileActions, DictActions])
            modified = []
            for a in self.settings_override:
                if "dict" in a:
                    modified.append(a["dict"])
                    vi[a["dict"]] = m.modify_object(a["action"],
                                                    vi[a["dict"]])
                elif "filename" in a:
                    m.modify(a["action"], a["filename"])
            for f in modified:
                vi[f].write_file(f)
    def test_strict_mode(self):
        modder = Modder(actions=[FileActions])
        d = {"Hello": "World"}
        mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
        self.assertRaises(ValueError, modder.modify, mod, d)

        #In non-strict mode, unknown actions are ignored.
        d = {"Hello": "World"}
        modder = Modder(actions=[FileActions], strict=False)
        modder.modify(mod, d)
        self.assertEqual(d, {"Hello": "World"})

        #File actions not supported
        modder = Modder()
        self.assertRaises(ValueError, modder.modify,
                          {'_file_create': {'content': 'Test data'}},
                          'test_file')
Exemple #3
0
    def correct(self):
        backup()
        actions = [{"file": "CONTCAR",
                    "action": {"_file_copy": {"dest": "POSCAR"}}},
                   {"dict": "INCAR",
                    "action": {"_set": {"ISTART": 1,
                                        "ALGO": "Normal",
                                        "NELMDL": 6,
                                        "BMIX": 0.001,
                                        "AMIX_MAG": 0.8,
                                        "BMIX_MAG": 0.001}}}]
        vi = VaspInput.from_directory(".")
        m = Modder(actions=[DictActions, FileActions])
        for a in actions:
            if "dict" in a:
                vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
            elif "file" in a:
                m.modify(a["action"], a["file"])
        vi["INCAR"].write_file("INCAR")

        return {"errors": ["Unconverged"], "actions": actions}
 def test_dict_modify(self):
     modder = Modder()
     d = {"Hello": "World"}
     mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'Hello': 'Universe'})
     mod = {'_unset': {'Hello': 1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World'})
     mod = {'_push': {'List': 1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1]})
     mod = {'_push': {'List': 2}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2]})
     mod = {'_inc': {'num': 5}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 5})
     mod = {'_inc': {'num': 5}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 10})
     mod = {'_rename': {'num': 'number'}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
     mod = {'_add_to_set': {'List': 2}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
     mod = {'_add_to_set': {'List': 3}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3], 'number': 10})
     mod = {'_add_to_set': {'number': 3}}
     self.assertRaises(ValueError, modder.modify, mod, d)
     mod = {'_pull': {'List': 1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [2, 3], 'number': 10})
     mod = {'_pull_all': {'List': [2, 3]}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [], 'number': 10})
     mod = {'_push_all': {'List': xrange(10)}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World',
                          'List': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
                          'number': 10})
     mod = {'_pop': {'List': 1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World',
                          'List': [0, 1, 2, 3, 4, 5, 6, 7, 8],
                          'number': 10})
     mod = {'_pop': {'List':-1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3, 4, 5, 6, 7, 8],
                          'number': 10})
     d = {}
     mod = {'_set': {'a->b->c': 100}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100}}})
     mod = {'_set': {'a->b->d': 200}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 200}}})
     mod = {'_set': {'a->b->d': 300}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 300}}})
     mod = {'_unset': {'a->b->d': 300}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100}}})
     mod = {'_push': {'a->e->f': 300}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100}, 'e': {'f': [300]}}})
     mod = {'_push_all': {'a->e->f': [100, 200]}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 100},
                                'e': {'f': [300, 100, 200]}}})
     mod = {'_inc': {'a->b->c': 2}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102},
                                'e': {'f': [300, 100, 200]}}})
     mod = {'_pull': {'a->e->f': 300}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [100, 200]}}})
     mod = {'_pull_all': {'a->e->f': [100, 200]}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': []}}})
     mod = {'_push_all': {'a->e->f': [101, 201, 301, 401]}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102},
                                'e': {'f': [101, 201, 301, 401]}}})
     mod = {'_pop': {'a->e->f': 1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102},
                                'e': {'f': [101, 201, 301]}}})
     mod = {'_pop': {'a->e->f':-1}}
     modder.modify(mod, d)
     self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [201, 301]}}})
 def test_file_modify(self):
     modder = Modder(actions=[FileActions])
     modder.modify({'_file_create': {'content': 'Test data'}}, 'test_file')
     modder.modify({'_file_copy': {'dest': 'test_file_copy'}}, 'test_file')
     modder.modify({'_file_copy': {'dest1': 'test_file_copy1',
                                   'dest2': 'test_file_copy2'}},
                   'test_file')
     modder.modify({'_file_move': {'dest': 'renamed_test_file'}},
                   'test_file')
     modder.modify({'_file_delete': {'mode': "actual"}},
                   'renamed_test_file')
     modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy')
     modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy1')
     modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy2')