bugged stringlengths 4 228k | fixed stringlengths 0 96.3M | __index_level_0__ int64 0 481k |
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def set_startup_hook(function=None): # TODO add pass | def set_startup_hook(function=None): # TODO addsys._jy_interpreter.startupHook = function def set_pre_input_hook(function=None): print "Not implemented: set_pre_input_hook", function | 447,800 |
def set_pre_input_hook(function=None): # TODO add pass | def set_pre_input_hook(function=None): # TODO add pass | 447,801 |
def set_completer(function=None): """set_completer([function]) -> None Set or remove the completer function. The function is called as function(text, state), for state in 0, 1, 2, ..., until it returns a non-string. It should return the next possible completion starting with 'text'.""" _completion_function = function ... | def set_completer(function=None): """set_completer([function]) -> None Set or remove the completer function. The function is called as function(text, state), for state in 0, 1, 2, ..., until it returns a non-string. It should return the next possible completion starting with 'text'.""" global _completer_function _comp... | 447,802 |
def complete_handler(buffer, cursor, candidates): for state in xrange(100): # TODO arbitrary, what's the number used by gnu readline? completion = None try: completion = function(buffer[:cursor], state) except: pass if completion: candidates.add(completion) else: break return 0 | def complete_handler(buffer, cursor, candidates): for state in xrange(100): # TODO arbitrary, what's the number used by gnu readline? completion = None try: completion = function(delimited, state) except: pass if completion: candidates.add(completion) else: break return 0 | 447,803 |
def complete_handler(buffer, cursor, candidates): for state in xrange(100): # TODO arbitrary, what's the number used by gnu readline? completion = None try: completion = function(buffer[:cursor], state) except: pass if completion: candidates.add(completion) else: break return 0 | def complete_handler(buffer, cursor, candidates): for state in xrange(100): # TODO arbitrary, what's the number used by gnu readline? completion = None try: completion = function(buffer[:cursor], state) except: pass if completion: candidates.add(completion) else: break return 0 | 447,804 |
def get_completer(): return _completion_function | def get_completer(): return _completer_function def _get_delimited(buffer, cursor): start = cursor for i in xrange(cursor-1, -1, -1): if buffer[i] in _completer_delims: break start = i return start, cursor | 447,805 |
def get_begidx(): # TODO add pass | def get_begidx(): # TODO addreturn _get_delimited(str(reader.cursorBuffer.buffer), reader.cursorBuffer.cursor)[0] | 447,806 |
def get_endidx(): # TODO add pass | def get_endidx(): # TODO addreturn _get_delimited(str(reader.cursorBuffer.buffer), reader.cursorBuffer.cursor)[1] | 447,807 |
def set_completer_delims(string): pass | def set_completer_delims(string): global _completer_delims, _completer_delims_set _completer_delims = string _completer_delims_set = set(string) | 447,808 |
def get_completer_delims(): pass | def get_completer_delims(): return _completer_delims | 447,809 |
def test_main(): test.test_support.run_unittest(SysTest, ShadowingTest) | def test_main(): test.test_support.run_unittest(SysTest, ShadowingTest, SyspathResourceTest) | 447,810 |
def test_main(): test_support.run_unittest(FunctionTypeTestCase, MethodHashCodeTestCase) | def test_main(): test_support.run_unittest(FunctionTypeTestCase, MethodHashCodeTestCase, SingleMethodInterfaceTestCase) | 447,811 |
def parse_and_bind(string): if string == "tab: complete": try: keybindings_field = _reader.class.getDeclaredField("keybindings") keybindings_field.setAccessible(True) keybindings = keybindings_field.get(_reader) COMPLETE = _reader.KEYMAP_NAMES.get('COMPLETE') if java.lang.reflect.Array.getShort(keybindings, 9) != COMPL... | def parse_and_bind(string): if string == "tab: complete": try: keybindings_field = _reader.class.getDeclaredField("keybindings") keybindings_field.setAccessible(True) keybindings = keybindings_field.get(_reader) COMPLETE = _reader.KEYMAP_NAMES.get('COMPLETE') if java.lang.reflect.Array.getShort(keybindings, 9) != COMPL... | 447,812 |
def parse_and_bind(string): if string == "tab: complete": try: keybindings_field = _reader.class.getDeclaredField("keybindings") keybindings_field.setAccessible(True) keybindings = keybindings_field.get(_reader) COMPLETE = _reader.KEYMAP_NAMES.get('COMPLETE') if java.lang.reflect.Array.getShort(keybindings, 9) != COMPL... | def parse_and_bind(string): if string == "tab: complete": try: keybindings_field = _reader.class.getDeclaredField("keybindings") keybindings_field.setAccessible(True) keybindings = keybindings_field.get(_reader) COMPLETE = _reader.KEYMAP_NAMES.get('COMPLETE') if java.lang.reflect.Array.getShort(keybindings, 9) != COMPL... | 447,813 |
def read_init_file(filename=None): warn("read_init_file: %s" % (filename,), NotImplementedWarning) | def read_init_file(filename=None): warn("read_init_file: %s" % (filename,), NotImplementedWarning, "module", 2) | 447,814 |
def remove_history_item(pos): if _history_list: _history_list.remove(pos) else: warn("Cannot remove history item at position: %s" % (pos,), SecurityWarning) | def remove_history_item(pos): if _history_list: _history_list.remove(pos) else: warn("Cannot remove history item at position: %s" % (pos,), SecurityWarning, stacklevel=2) | 447,815 |
def set_pre_input_hook(function=None): warn("set_pre_input_hook %s" % (function,), NotImplementedWarning) | def set_pre_input_hook(function=None): warn("set_pre_input_hook %s" % (function,), NotImplementedWarning, stacklevel=2) | 447,816 |
def test_main(): test_support.run_unittest(InstantiationTest, BeanTest, SysIntegrationTest, IOTest, JavaReservedNamesTest, PyReservedNamesTest, ImportTest, ColorTest, TreePathTest, BigNumberTest, JavaStringTest, JavaDelegationTest, SecurityManagerTest, JavaWrapperCustomizationTest, SerializationTest) | def test_main(): test_support.run_unittest(InstantiationTest, BeanTest, SysIntegrationTest, IOTest, JavaReservedNamesTest, PyReservedNamesTest, ImportTest, ColorTest, TreePathTest, BigNumberTest, JavaStringTest, JavaDelegationTest, SecurityManagerTest, JavaWrapperCustomizationTest, SerializationTest, UnicodeTest) | 447,817 |
def serve_forever(self): """Handle one request at a time until doomsday.""" while 1: self.handle_request() | def serve_forever(self): """Handle one request at a time until doomsday.""" while 1: self.handle_request() | 447,818 |
def handle_request(self): """Handle one request, possibly blocking.""" try: request, client_address = self.get_request() except socket.error: return if self.verify_request(request, client_address): try: self.process_request(request, client_address) except: self.handle_error(request, client_address) self.close_request(r... | def handle_request(self): """Handle one request, possibly blocking.""" try: os.remove(fn) except os.error: pass testfiles[:] = [] def testloop(proto, servers, hdlrcls, testfunc): for svrcls in servers: addr = pickaddr(proto) if verbose: print "ADDR =", addr print "CLASS =", svrcls t = ServerThread(addr, svrcls, hdlrcl... | 447,819 |
def handle_request(self): """Handle one request, possibly blocking.""" try: request, client_address = self.get_request() except socket.error: return if self.verify_request(request, client_address): try: self.process_request(request, client_address) except: self.handle_error(request, client_address) self.close_request(r... | def handle_request(self): """Handle one request, possibly blocking.""" try: request, client_address = self.get_request() except socket.error: return if self.verify_request(request, client_address): try: self.process_request(request, client_address) except: self.handle_error(request, client_address) self.close_request(r... | 447,820 |
def check_list(self, control, results, initial): for result in results: try: len(result) except: print result self.assertEquals(len(control), len(result), "%s is wrong for %s" % (type(result), initial)) for pvalue, jvalue in zip(control, result): self.assertEquals(pvalue, jvalue) | def _arraylist_of(self, xs): """ Converts a python list to a java.util.ArrayList """ a = ArrayList() a.addAll( xs ) return a def check_list(self, control, results, list_type_names, initial, test_name): for result, type_name in zip(results, list_type_names): try: len(result) except: print result self.assertEquals(len(c... | 447,821 |
def check_list(self, control, results, initial): for result in results: try: len(result) except: print result self.assertEquals(len(control), len(result), "%s is wrong for %s" % (type(result), initial)) for pvalue, jvalue in zip(control, result): self.assertEquals(pvalue, jvalue) | def check_list(self, control, results, initial): for result in results: try: len(result) except: print result self.assertEquals(len(control), len(result), "%s is wrong for %s" % (type(result), initial)) for pvalue, jvalue in zip(control, result): self.assertEquals(pvalue, jvalue) | 447,822 |
def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | 447,823 |
def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | 447,824 |
def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | def _list_op_test(self, initial_value, op_func, check_value): """ Tests a list operation | 447,825 |
def test_get_integer(self): initial_value = range(0, 5) | def test_get_integer(self): initial_value = range(0, 5) | 447,826 |
def _f(xs): xs[index] = 100 | def _f(xs): xs[index] = 100 | 447,827 |
def test_set_slice(self): initial_value = range(0, 10) | def test_set_slice(self): initial_value = range(0, 10) | 447,828 |
def _f(xs): xs[i:j:k] = v | def _f(xs): xs[i:j:k] = v | 447,829 |
def _f(xs): del xs[index] | def _f(xs): del xs[index] | 447,830 |
def test_del_slice(self): initial_value = range(0,10) | def test_del_slice(self): initial_value = range(0,10) | 447,831 |
def _f(xs): del xs[i:j:k] | def _f(xs): del xs[i:j:k] | 447,832 |
def size(self): return self._jffi_type.size | def size(self): return self._jffi_type.size | 447,833 |
def sizeof(type): if hasattr(type, '_jffi_type'): return type._jffi_type.size else: raise TypeError("this type has no size") | def sizeof(type): if hasattr(type, '_jffi_type'): return type._jffi_type.size() else: raise TypeError("this type has no size") | 447,834 |
def alignment(type): return type._jffi_type.alignment | def alignment(type): return type._jffi_type.alignment() | 447,835 |
def test_java_serialization(self): date_list = [Date(), Date()] output = ByteArrayOutputStream() serializer = ObjectOutputStream(output) serializer.writeObject(date_list) serializer.close() | def test_java_serialization(self): date_list = [Date(), Date()] output = ByteArrayOutputStream() serializer = ObjectOutputStream(output) serializer.writeObject(date_list) serializer.close() | 447,836 |
def characters(self, char, start, len): self._cont_handler.characters(String(char, start, len).getBytes('utf-8').tostring().decode('utf-8')) | def characters(self, char, start, len): self._cont_handler.characters(String(char, start, len).getBytes('utf-8').tostring().decode('utf-8')) | 447,837 |
def ignorableWhitespace(self, char, start, len): self._cont_handler.ignorableWhitespace(String(char, start, len).getBytes('utf-8').tostring().decode('utf-8')) | def ignorableWhitespace(self, char, start, len): self._cont_handler.ignorableWhitespace(String(char, start, len).getBytes('utf-8').tostring().decode('utf-8')) | 447,838 |
def extract_ov_meths(jcl,envl_class): meths = java.lang.Class.getDeclaredMethods(jcl) names = [ m.name for m in meths] meth_dict = {} for name in names: if name.startswith('ov_') and not meth_dict.has_key(name): meth_dict[name] = envl_class(name,[ m for m in meths if m.name == name ]) return meth_dict | def extract_ov_meths(jcl,envl_class): meths = java.lang.Class.getDeclaredMethods(jcl) names = [ m.name for m in meths] meth_dict = {} for name in names: if name.startswith('ov_') and not meth_dict.has_key(name): meth_dict[name] = envl_class(name,[ m for m in meths if m.name == name ]) return meth_dict | 447,839 |
def printout(meth_dict,lbl,rng,args): for i in rng: print meth_dict['ov_%s%s' % (lbl,i)](jo,args) | def printout(meth_dict,lbl,rng,args): for i in rng: print meth_dict['ov_%s%s' % (lbl,i)](jo,args) | 447,840 |
def printout(meth_dict,lbl,rng,args): for i in rng: print meth_dict['ov_%s%s' % (lbl,i)](jo,args) | def printout(meth_dict,lbl,rng,args): for i in rng: print meth_dict['ov_%s%s' % (lbl,i)](jo,args) | 447,841 |
def __init__(self, source): if isinstance(source, str): javasax.InputSource.__init__(self, source) elif hasattr(source, "read"):#file like object f = source javasax.InputSource.__init__(self, FilelikeInputStream(f)) if hasattr(f, "name"): self.setSystemId(f.name) else:#xml.sax.xmlreader.InputSource object #Use byte str... | def __init__(self, source): if isinstance(source, basestring): javasax.InputSource.__init__(self, source) elif hasattr(source, "read"):#file like object f = source javasax.InputSource.__init__(self, FilelikeInputStream(f)) if hasattr(f, "name"): self.setSystemId(f.name) else:#xml.sax.xmlreader.InputSource object #Use b... | 447,842 |
def test_main(): test_support.run_unittest(ReferencesTestCase) | def test_main(): test_support.run_unittest(ReferencesTestCase, ArgsTestCase) | 447,843 |
def test_lock_type(self): "thread.LockType should exist" t = thread.LockType self.assertEquals(t, type(thread.allocate_lock()), "thread.LockType has wrong value") | def test_lock_type(self): """thread.LockType should exist""" t = thread.LockType self.assertEquals(t, type(thread.allocate_lock()), "thread.LockType has wrong value") | 447,844 |
def comment(self, char, start, len): print "Content handler is %s" % self._cont_handler.__class__ self._cont_handler.comment(unicode(String(char, start, len))) | def comment(self, char, start, len): self._cont_handler.comment(unicode(String(char, start, len))) | 447,845 |
def on_disconnected(self): self._logger.warning('TCP/IP connection lost.') | def on_disconnected(self): self._logger.warning('TCP/IP connection lost.') | 447,846 |
def send(self, destination=None, message='', headers=None, **keyword_headers): """Add message to local queue for sending to MSG server. @param destination: An MSG topic or queue, e.g. /topic/dashboard.test. @param message: A string or dictionary of key-value pairs. @param headers: A dictionary of headers. @param keywo... | def send(self, destination=None, message='', headers=None, **keyword_headers): """Add message to local queue for sending to MSG server. @param destination: An MSG topic or queue, e.g. /topic/dashboard.test. @param message: A string or dictionary of key-value pairs. @param headers: A dictionary of headers. @param keywo... | 447,847 |
def _disconnect(self): """Disconnects (quietly) from MSG server if not already disconnected.""" cx = self._cx if cx is not None: self._log(logging.DEBUG, 'Disconnecting') self._cx = None if cx.is_connected(): try: cx.disconnect() except Exception: self._log(logging.WARNING, 'Exception on disconnect.', exc_info=True) se... | def _disconnect(self): """Disconnects (quietly) from MSG server if not already disconnected.""" cx = self._cx if cx is not None: self._log(logging.DEBUG, 'Disconnecting') self._cx = None if cx.is_connected(): try: cx.disconnect() except Exception: self._log(logging.DEBUG, 'Exception on disconnect.', exc_info=True) self... | 447,848 |
def run(self): """Send messages, connecting as necessary and disconnecting after idle_timeout seconds. """ # indicates time in seconds since last connect/send attempt idle_time = 0 # indicates time in seconds before next connect/send attempt backoff_time = 0 # run unless should_stop and (queue empty or backing off) whi... | def run(self): """Send messages, connecting as necessary and disconnecting after idle_timeout seconds. """ # indicates time in seconds since last connect/send attempt idle_time = 0 # indicates time in seconds before next connect/send attempt backoff_time = 0 # run unless should_stop and (queue empty or backing off) whi... | 447,849 |
def findSongBySize(self, size): cursor = self.db.cursor() query = cursor.execute( self.querystring + " where tracks.filesize = " + size ) results = cursor.fetchall() return self.rowsToSongs( results ) | def findSongBySize(self, size): cursor = self.db.cursor() query = cursor.execute( self.querystring + " where tracks.filesize = " + str(size) ) results = cursor.fetchall() return self.rowsToSongs( results ) | 447,850 |
def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | 447,851 |
def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | 447,852 |
def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | def correlateSong( self, song, confirm, fastAndLoose, promptForDisambiguate ): match = None matches = self.parser.findSongBySize( song.size ); matchcount = len(matches) # no results if matchcount == 0: print "\t no matches found" self.zeroMatches = self.zeroMatches + 1 # full match elif matchcount == 1: match = match... | 447,853 |
def __init__(self, location) self.doc = libxml2.parseFile( location ) self.xpathContext = doc.xpathNewContext() return | def __init__(self, location): self.doc = libxml2.parseFile( location ) self.xpathContext = doc.xpathNewContext() return | 447,854 |
def getSongs(self): return getPlaylistFiles('Library') | def getSongs(self): return self.getPlaylistFiles('Library') | 447,855 |
def __init__(self, WMPSong): self.wmpNode = WMPSong self.artist = WMPSong.getItemInfo("WM/AlbumArtist") self.album = WMPSong.getItemInfo("WM/AlbumTitle") self.title = WMPSong.name self.size = WMPSong.getItemInfo("FileSize") self.rating = WMPSong.getItemInfo("UserRating") self.playcount = WMPSong.getItemInfo("UserPlayco... | def __init__(self, WMPSong): self.wmpNode = WMPSong self.artist = WMPSong.getItemInfo("WM/AlbumArtist") self.album = WMPSong.getItemInfo("WM/AlbumTitle") self.title = WMPSong.name self.size = WMPSong.getItemInfo("FileSize") try: self.rating = int(WMPSong.getItemInfo("UserRating")) except ValueError: print WMPSong.getIt... | 447,856 |
def showUsage(self): print "iTunesToRhythm <path to ItunesMusicLibrary.xml> <path to rhythmdb.xml> | def showUsage(self): print "iTunesToRhythm <path to ItunesMusicLibrary.xml> <path to rhythmdb.xml>" | 447,857 |
def setRating( self, rating): ratingValueNodes = self.xmlNode.xpathEval("integer[preceding-sibling::* = 'Rating'][1]") if len( ratingValueNodes ) == 0: newRatingKeyNode= libxml2.newNode("key") newRatingKeyNode.setContent("rating") ratingValueNode = libxml2.newNode("integer") newRatingKeyNode.addSibling( ratingValueNo... | def setRating( self, rating): ratingValueNodes = self.xmlNode.xpathEval("integer[preceding-sibling::* = 'Rating'][1]") if len( ratingValueNodes ) == 0: newRatingKeyNode= libxml2.newNode("key") newRatingKeyNode.setContent("Rating") ratingValueNode = libxml2.newNode("integer") newRatingKeyNode.addSibling( ratingValueNo... | 447,858 |
def setPlaycount(self, playcount): self.wmpNode.setItemInfo("UserPlaycount", rating) | def setPlaycount(self, playcount): self.wmpNode.setItemInfo("UserPlaycount", rating) | 447,859 |
def set_frame(self, frame=None, focus=False, init=False): if frame is None: frame = self.frame | def set_frame(self, frame=None, focus=False, init=False): if frame is None: frame = self.frame | 447,860 |
def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | 447,861 |
def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | 447,862 |
def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | 447,863 |
def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | def equivalent_sites(self, scaled_positions, ondublicates='error', symprec=1e-3): """Returns the scaled positions and all their equivalent sites. | 447,864 |
def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | 447,865 |
def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | def read_aims_output(filename, index = -1): """ Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc. """ from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs molecular_dynamics = False f... | 447,866 |
def restart_load(self): """Method which is called upon restart.""" # Try to read sorting file if os.path.isfile('ase-sort.dat'): self.sort = [] self.resort = [] file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.appen... | def restart_load(self): """Method which is called upon restart.""" # Try to read sorting file if os.path.isfile('ase-sort.dat'): self.sort = [] self.resort = [] file = open('ase-sort.dat', 'r') lines = file.readlines() file.close() for line in lines: data = line.split() self.sort.append(int(data[0])) self.resort.appen... | 447,867 |
def get_dipole_moment(self, atoms): """Returns total dipole moment of the system.""" self.update(atoms) return self.dipole | def get_dipole_moment(self, atoms): """Returns total dipole moment of the system.""" self.update(atoms) return self.dipole | 447,868 |
def get_calculator_gpaw(): calc = GPAW(h=0.2, mode='lcao', basis='szp(dzp)', nbands=-5, xc='LDA', width=0.1, mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0), poissonsolver=PoissonSolver(nn='M', relax='GS'), convergence={'energy':1e-4, 'bands':-3}, stencils=(3, 3), txt='neb.txt') return calc | def get_calculator_gpaw(): calc = GPAW(h=0.2, mode='lcao', basis='szp(dzp)', nbands=-5, xc='LDA', width=0.1, mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0), poissonsolver=PoissonSolver(nn='M', relax='GS'), convergence={'energy':1e-4, 'bands':-3}, stencils=(3, 3), txt='neb.txt') return calc | 447,869 |
def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | def cut(atoms, a=(1,0,0), b=(0,1,0), c=(0,0,1), origo=(0,0,0), nlayers=None, extend=1.0, tolerance=0.001): """Cuts out a cell defined by *a*, *b*, *c* and *origo* from a sufficiently repeated copy of *atoms*. Typically, this function is used to create slabs of different sizes and orientations. The vectors *a*, *b* and... | 447,870 |
def read_only_atoms(self,ncfile): '''read only the atoms from an existing netcdf file. Used to initialize a calculator from a ncfilename. | def read_only_atoms(self,ncfile): '''read only the atoms from an existing netcdf file. Used to initialize a calculator from a ncfilename. | 447,871 |
def read_only_atoms(self,ncfile): '''read only the atoms from an existing netcdf file. Used to initialize a calculator from a ncfilename. | def read_only_atoms(self,ncfile): '''read only the atoms from an existing netcdf file. Used to initialize a calculator from a ncfilename. | 447,872 |
def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 447,873 |
def set_kpts(self, kpts): ''' set the kpt grid. | def set_kpts(self, kpts): ''' set the kpt grid. | 447,874 |
def set_kpts(self, kpts): ''' set the kpt grid. | def set_kpts(self, kpts): ''' set the kpt grid. | 447,875 |
def get_ensemble_coefficients(self): ''' adapted from ASE/dacapo.py def GetEnsembleCoefficients(self): self.Calculate() E = self.GetPotentialEnergy() xc = self.GetNetCDFEntry('EnsembleXCEnergies') Exc = xc[0] exc_c = self.GetNetCDFEntry('EvaluateCorrelationEnergy') exc_e = self.GetNetCDFEntry('EvaluateExchangeEnergy')... | def get_ensemble_coefficients(self): ''' adapted from ASE/dacapo.py def GetEnsembleCoefficients(self): self.Calculate() E = self.GetPotentialEnergy() xc = self.GetNetCDFEntry('EnsembleXCEnergies') Exc = xc[0] exc_c = self.GetNetCDFEntry('EvaluateCorrelationEnergy') exc_e = self.GetNetCDFEntry('EvaluateExchangeEnergy')... | 447,876 |
def __init__(self, energy, forces, stress, magmoms, atoms): """Save energy, forces and stresses for the current configuration.""" self.energy = energy self.forces = np.array(forces, float) self.stress = np.array(stress, float) self.magmoms = np.array(magmoms, float) self.atoms = atoms.copy() | def __init__(self, energy, forces, stress, magmoms, atoms): """Save energy, forces and stresses for the current configuration.""" self.energy = energy if forces is not None: forces = np.array(forces, float) self.forces = forces if stress is not None: stress = np.array(stress, float) self.stress = stress if magmoms is n... | 447,877 |
def execute_external_dynamics(self, nc=None, txt=None, stoppfile='stop', stopprogram=None): ''' Implementation of the stay alive functionality with socket communication between dacapo and python. Known limitations: It is not possible to start 2 independent Dacapo calculators from the same python process, since the pyt... | def execute_external_dynamics(self, nc=None, txt=None, stoppfile='stop', stopprogram=None): ''' Implementation of the stay alive functionality with socket communication between dacapo and python. Known limitations: It is not possible to start 2 independent Dacapo calculators from the same python process, since the pyt... | 447,878 |
def __init__(self, label='dftb', write_dftb=False, charge=0.0, include_dispersion=False, do_spin_polarized=False, unpaired_electrons=0.0, fermi_temperature=0.0, scc=False, kpt_n11=1, kpt_n12=0, kpt_n13=0, kpt_n21=0, kpt_n22=1, kpt_n23=0, kpt_n31=0, kpt_n32=0, kpt_n33=1, kpt_s1=0.0, kpt_s2=0.0, kpt_s3=0.0, md_dftb=False... | def __init__(self, label='dftb', write_dftb=False, charge=0.0, include_dispersion=False, do_spin_polarized=False, unpaired_electrons=0.0, fermi_temperature=0.0, scc=False, kpt_n11=1, kpt_n12=0, kpt_n13=0, kpt_n21=0, kpt_n22=1, kpt_n23=0, kpt_n31=0, kpt_n32=0, kpt_n33=1, kpt_s1=0.0, kpt_s2=0.0, kpt_s3=0.0, md_dftb=False... | 447,879 |
def valid_ascii_debug(x): return (x in ['Off', 'MediumLevel', 'HighLevel']) | def valid_ascii_debug(x): return (x.strip() in ['Off', 'MediumLevel', 'HighLevel']) | 447,880 |
def valid_electronic_minimization(x): valid_keys = ['method', 'diagsperband'] for key in x: if key not in valid_keys: return False elif key == 'method': if x[key] not in ['resmin', 'eigsolve', 'rmm-diis']: return False elif key == 'diagsperband': if not valid_int(x[key]): return False return True | def valid_electronic_minimization(x): valid_keys = ['method', 'diagsperband'] for key in x: if key not in valid_keys: return False elif key == 'method': if x[key] not in ['resmin', 'eigsolve', 'rmm-diis']: return False elif key == 'diagsperband': if not (valid_int(x[key]) or x[key] is None): return False return True | 447,881 |
def write_aims(filename, atoms): """Method to write FHI-aims geometry files. Writes the atoms positions and constraints (only FixAtoms is supported at the moment). """ from ase.constraints import FixAtoms, FixCartesian import numpy as np if isinstance(atoms, (list, tuple)): if len(atoms) > 1: raise RuntimeError("Don... | def write_aims(filename, atoms): """Method to write FHI-aims geometry files. Writes the atoms positions and constraints (only FixAtoms is supported at the moment). """ from ase.constraints import FixAtoms, FixCartesian import numpy as np if isinstance(atoms, (list, tuple)): if len(atoms) > 1: raise RuntimeError("Don... | 447,882 |
def get_magnetic_moments(self, atoms): if self.int_params['lorbit']>=10 or self.list_params['rwigs']: self.update(atoms) return self.magnetic_moments else: raise RuntimeError( "The combination %s for lorbit with %s for rwigs not supported to calculate magnetic moments" % (p['lorbit'], p['rwigs'])) | def get_magnetic_moments(self, atoms): if self.int_params['lorbit']>=10 or self.list_params['rwigs']: self.update(atoms) return self.magnetic_moments else: raise RuntimeError( "The combination %s for lorbit with %s for rwigs not supported to calculate magnetic moments" % (p['lorbit'], p['rwigs'])) | 447,883 |
def __eq__(self, other): """Chech whether *self* and *other* refer to the same spacegroup number and setting.""" return self.no == other.no and self.setting == other.setting | def __eq__(self, other): """Chech whether *self* and *other* refer to the same spacegroup number and setting.""" return self.no == other.no and self.setting == other.setting | 447,884 |
def _read_datafile_entry(spg, no, symbol, setting, f): """Read space group data from f to spg.""" spg._no = no spg._symbol = symbol.strip() spg._setting = setting spg._centrosymmetric = bool(f.readline().split()[1]) # primitive vectors f.readline() spg._scaled_primitive_cell = np.array([map(float, f.readline().split())... | def _read_datafile_entry(spg, no, symbol, setting, f): """Read space group data from f to spg.""" spg._no = no spg._symbol = symbol.strip() spg._setting = setting spg._centrosymmetric = bool(int(f.readline().split()[1])) # primitive vectors f.readline() spg._scaled_primitive_cell = np.array([map(float, f.readline().spl... | 447,885 |
def set_psp_database(self, xc=None): ''' get the xc-dependent psp database | def set_psp_database(self, xc=None): ''' get the xc-dependent psp database | 447,886 |
def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50, args=()): | def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50, args=()): | 447,887 |
def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50, args=()): | def _line_search(self, func, myfprime, xk, pk, gfk, old_fval, old_old_fval, maxstep=.2, c1=.23, c2=0.46, xtrapl=1.1, xtrapu=4., stpmax=50, args=()): | 447,888 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | defstep(self,stp,f,g,c1,c2,xtol,isave,dsave):ifself.task[:5]=='START': | 447,889 |
def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | def step(self, stp, f, g, c1, c2, xtol, isave, dsave): if self.task[:5] == 'START': | 447,890 |
def update(self, stx, fx, gx, sty, fy, gy, stp, fp, gp, bracket, stpmin, stpmax): sign = gp * (gx / abs(gx)) | defupdate(self,stx,fx,gx,sty,fy,gy,stp,fp,gp,bracket,stpmin,stpmax):sign=gp*(gx/abs(gx)) | 447,891 |
def update(self, stx, fx, gx, sty, fy, gy, stp, fp, gp, bracket, stpmin, stpmax): sign = gp * (gx / abs(gx)) | defupdate(self,stx,fx,gx,sty,fy,gy,stp,fp,gp,bracket,stpmin,stpmax):sign=gp*(gx/abs(gx)) | 447,892 |
def determine_step(self, stp): dr = stp - self.old_stp if pymax(self.pk) * dr > self.maxstep: dr /= (pymax(self.pk) * dr / self.maxstep) stp = self.old_stp + dr return stp | def determine_step(self, stp): dr = stp - self.old_stp if abs(pymax(self.pk) * dr) > self.maxstep: dr /= abs((pymax(self.pk) * dr) / self.maxstep) stp = self.old_stp + dr return stp | 447,893 |
def set(self, **kwargs): '''set a parameter | def set(self, **kwargs): '''set a parameter | 447,894 |
def read(ncfile): '''return atoms and calculator from ncfile >>> atoms, calc = read('co.nc') ''' calc = Jacapo(ncfile) atoms = calc.get_atoms() #this returns a copy return (atoms, calc) | def read(ncfile): '''return atoms and calculator from ncfile >>> atoms, calc = read('co.nc') ''' calc = Jacapo(ncfile) atoms = calc.get_atoms() #this returns a copy return (atoms, calc) | 447,895 |
def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=logging.WARN, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 447,896 |
def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 447,897 |
def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 447,898 |
def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | def __init__(self, nc='out.nc', outnc=None, debug=0, stay_alive=False, **kwargs): ''' Initialize the Jacapo calculator | 447,899 |
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