sampledoc

Source code for bonds

"""
Class data structures for 2, 3, 4 point groupings of Particle objects
"""
import copy, sys

[docs]class Bond: """ Data structure for describing any 2-point associatiaon of Particle-s """ def __init__(self, pgid1=0, pgid2=0, length=0.0, type="blank"): """ Constructor for a general bond. Checks for types in arguments and throws a TypeError when appropriate Args: pgid1 (int) GlobalID of Particle object in bond pgid2 (int) GlobalID of Particle object in bond length (float) Cartesian length of bond type (str) Charge value in units of [e] """ if isinstance(pgid1, int): self.pgid1 = pgid1 else: print "1st arg should be int" raise TypeError if isinstance(pgid2, int): self.pgid2 = pgid2 else: print "2nd arg should be int type" raise TypeError if isinstance(length, float): self.length = length else: print "3rd arg should be float value" raise TypeError if isinstance(type, str): self.type = type else: print "4th arg should be string value" raise TypeError self.lmpindx = 0 self.g_indx = 0 def __del__(self): """ Destructor, clears object memory """ del self.pgid1 del self.pgid2 del self.length del self.type del self.lmpindx del self.g_indx def __contains__(self, pgid): """ 'Magic' method implementing 'in' keyword. Args: pgid (int) Particle GID to check against 'held' IDs """ if ( (pgid == self.pgid1) or (pgid == self.pgid2) ): return True else: return False
[docs] def set_lmpindx(self,lmpindx): """ Set bond type index for lammps """ self.lmpindx = lmpindx
[docs] def get_lmpindx(self): """ Return bond type index for lammps """ return self.lmpindx
[docs] def set_g_indx(self,g_indx): """ Set bond type index for gromacs """ self.g_indx = g_indx
[docs] def get_g_indx(self): """ Return bond type index for gromacs """ return self.g_indx
def __str__(self): """ 'Magic' method for printng contents """ return " %s - %s %s "%(self.pgid1,self.pgid2,self.type )
[docs]class BondContainer: """ Main data structure for holding Bond objects. Map of global bond ID (integer) to Bond object instances """ def __init__(self, idList=[], verbose=False): """ Constructor: sets up a dictionary for indexing 'Bond' objects Args: idList (list): of bond IDs. If empty then ID starts at 1. If not empty then ID's (keys) are inititalized with Bond objects verbose (bool): flag for printing status/debug info """ self.verbose=verbose self.bonds=dict() # Creates empty dict struc self.bonds={key: Bond() for key in idList} # Creates empty Bond objs # if idList not empty if len(idList) == 0: # If list not set in constructor arg self.maxgid=0 # default=0 if idList empty else: # self.maxgid=max(idList) # take max in list for maxgid def __del__(self): """ Destructor, clears dictionary memory """ if self.verbose: print "Cleaning particle container" del self.bonds del self.maxgid
[docs] def clear(self): """ Clears bonds out of BondContainer """ self.maxgid = 0 self.bonds=dict() # Creates empty dict struc
def __len__(self): """ 'Magic' method for returning size of container """ return len(self.bonds) def __str__(self): """ 'Magic' method for printng contents """ bondStr="\n Contains bond objects: \n" for gid in self.bonds: bondStr += " %d : %s \n"%(gid,self.bonds[gid] ) return bondStr
[docs] def keys(self): """ Return list of all ptcl IDs (keys) currently in container """ keyList = self.bonds.keys() return keyList
def __setitem__(self, gid, bond): """ 'Magic' method implementing obj[]=value operator Performs deep copy of value so container is managing memory """ if gid in self.bonds.keys(): self.bonds[gid]=copy.deepcopy(bond) else: print "Cannot add bond object to non-existent ID" sys.exit(3) def __getitem__(self, gid): """ 'Magic' method implementing obj[] operator Operations on returned elements change container """ return self.bonds[gid] def __delitem__(self, gid): """ 'Magic' method implementing del obj[] operator """ del self.bonds[gid] def __iter__(self): """ 'Magic' method implementing (for x in 'this').... """ # return iter(self.bonds) return self.bonds.iteritems() def __call__(self, idSubList=None): """ Callable magic method. Returns iterator to subset bonds dictionary Args: idSubList (list) list of pid-s of particle objects to be returned Returns: iterator to subset of particle dictionary """ subGroupDct = dict() if idSubList != None: for gid, bondObj in self.bonds.iteritems(): if gid in idSubList: subGroupDct[gid] = bondObj return subGroupDct.iteritems() else: print "Callable BondContainer requires a list of subgroup bond IDs" sys.exit(3) def __contains__(self, gid): """ 'Magic' method implementing in keyword (key in obj').... """ return gid in self.bonds
[docs] def hasBond(self, bondList): """ Check the ptcl IDs in bondList for any bond in container that is similar eg bond 1-2 is same as bond 2-1 Args: (list) ptcl IDs defining bond to search for Returns: (bool) is bond in container """ for gid, bondObj in self.bonds.iteritems(): p1 = bondObj.pgid1 p2 = bondObj.pgid2 if ((p1 in bondList) and (p2 in bondList)): return True return False
def __iadd__(self, other): """ 'Magic' method to implement the '+=' operator Compare global IDs of bonds and reassign globalIDs for bond container using the max ID between the two lists Note: for now this reassigns ID always """ keys1 = self.bonds.keys() # global IDs in this object keys2 = other.bonds.keys() # global IDs in object being added bothkeys = keys1 + keys2 # List of all keys if len(bothkeys) > 0: # If keys not empty... proceed self.maxgid = max(keys1 + keys2) # find max globalID in keys, set this object maxID for ptclkey2 in other.bonds: self.put(other.bonds[ptclkey2]) return self
[docs] def put(self, bond): """ Append 'Bond' object to this container. Updates globalID for container by incrementing the maxgid member Args: ptcl (Particle) correctly initialized Particle object NOTE: (1) One can imagine extra conditions on bonds inserted (2) This could check for uniqueness of all globalID's and throw error for copies """ if isinstance(bond, Bond): self.maxgid += 1 self.bonds[self.maxgid] = copy.deepcopy(bond) else: print "Attempting to add non-Bond type to container" raise TypeError
[docs] def replacePtclIDs(self, idFromTo): """ Replace ptclIDs given a dictionary of ID changes # eg {1:3, 3:5, 2:20...} Args: idFromTo (dict) map of ID changes """ fromIDs = idFromTo.keys() for gid in self.bonds: bond = self.bonds[gid] # Bond object pgid1 = bond.pgid1 # ptcl1 in bond pgid2 = bond.pgid2 # ptcl2 in bond if pgid1 in fromIDs: toID = idFromTo[pgid1] bond.pgid1 = toID if pgid2 in fromIDs: toID = idFromTo[pgid2] bond.pgid2 = toID
[docs] def getTypeInfoDict(self): """ Return a map of type to typeIndex Method assigns a type index and checkes for consistency Returns: dictionary """ # Look for types and get unique list typeList = list() for gid, bondObj in self.bonds.iteritems(): bondType = bondObj.type typeList.append(bondType) typeList = list(set(typeList)) # Generate list of unique type for keys to initialize dictionary typeIndexDict = {key:index+1 for index, key in enumerate(typeList)} # dict for typeIndex if self.verbose: print "Unique types = ", typeList print "typeIndexDict = ", typeIndexDict # Pack yypeIndex to new dictionary typeInfoDict = dict() for key in typeIndexDict: index = typeIndexDict[key] typeInfoDict[key] = index return typeInfoDict