예제 #1
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def get_population(Optimizer):
    """
	Function to generate a population of structures.
	Inputs:
		Optimizer = structopt_stem Optimizer class object
	Outputs:
		pop = List of structopt_stem Individual class objects containing new structures.
	"""
    index1 = 0
    pop = []
    for i in range(Optimizer.nindiv):
        if Optimizer.structure == 'Defect':
            individ = get_defect_indiv(Optimizer)
        elif Optimizer.structure == 'Surface':
            individ = get_surface_indiv(Optimizer)
        elif Optimizer.structure == 'Crystal':
            individ = get_crystal_indiv(Optimizer)
        else:
            if 'sphere' in Optimizer.generate_flag:
                ind = gen_pop_sphere(Optimizer.atomlist,Optimizer.size)
            else:
                ind = gen_pop_box(Optimizer.atomlist,Optimizer.size)
            individ = Individual(ind)
        individ.index = index1
        if Optimizer.genealogy: 
            individ.history_index = repr(index1)
        Optimizer.output.write('Generated cluster individual with natoms = '+
            repr(individ[0].get_number_of_atoms())+'\n')
        pop.append(individ)
        index1=index1+1
    # Generate new atomlist concentrations based on cluster+box
    if Optimizer.structure == 'Defect':
        if Optimizer.alloy:
            concents=[]
            for ind in pop:
                cs=[]
                for sym,c,u,m in Optimizer.atomlist:
                    sylen=[atm for atm in ind[0] if atm.symbol==sym]
                    cs.append(len(sylen))
                concents.append(cs)
            natmlist=[0]*len(Optimizer.atomlist)
            for i in range(len(concents[0])):
                alls=[cs[i] for cs in concents]
                avgall=int(sum(alls)/len(alls))
                if avgall>=Optimizer.atomlist[i][1]:
                    natmlist[i]=(Optimizer.atomlist[i][0], avgall,
                        Optimizer.atomlist[i][2],Optimizer.atomlist[i][3])
                else:
                    natmlist[i]=(Optimizer.atomlist[i][0], Optimizer.atomlist[i][1],
                        Optimizer.atomlist[i][2],Optimizer.atomlist[i][3])
        else:
            natmlist=[0]*len(Optimizer.atomlist)
            for i in range(len(Optimizer.atomlist)):
                atms1=[inds for inds in pop[0][0] if inds.symbol==Optimizer.atomlist[i][0]]
                natmlist[i]=(Optimizer.atomlist[i][0], len(atms1),Optimizer.atomlist[i][2],
                    Optimizer.atomlist[i][3])
        Optimizer.atomlist=natmlist
        Optimizer.output.write('\n\nNew atomlist concentrations based on cluster+box = '+
            repr(Optimizer.atomlist)+'\n')
    return pop
예제 #2
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         Optimizer.output.write('WARNING: Trouble reading file: {0}'.format(Optimizer.files[i].name),exc_info=True)
         Optimizer.output.write('Error: {0}'.format(e))
         Optimizer.output.flush()
         Optimizer.nindiv-=1
     if successflag:
         Optimizer.output.write('Found good individual = {0}\n'.format(indiv))
         if Optimizer.structure == 'Defect':
             individ = get_defect_restart_indiv(Optimizer,indiv)
         elif Optimizer.structure == 'Surface':
             individ = get_surface_restart_indiv(Optimizer, indiv)
         else:
             cell = indiv.get_cell()
             if cell[0][0] == 1.0:
                indiv.set_cell([Optimizer.size,Optimizer.size,Optimizer.size])
             individ = Individual(indiv)
         individ.index = index1
         if Optimizer.genealogy: 
         	individ.history_index = repr(index1)
         pop.append(individ)
         index1 = index1+1
 if len(pop) == 0:
     raise RuntimeError('Unable to load any structures for Restart')
 # Generate new atomlist concentrations based on cluster+box
 if Optimizer.structure == 'Defect':
     if Optimizer.alloy:
         concents=[]
         for ind in pop:
             cs=[]
             for sym,c,u,m in Optimizer.atomlist:
                 sylen=[atm for atm in ind[0] if atm.symbol==sym]
                 cs.append(len(sylen))
예제 #3
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def get_population(Optimizer):
    """
	Function to generate a population of structures.
	Inputs:
		Optimizer = structopt_stem Optimizer class object
	Outputs:
		pop = List of structopt_stem Individual class objects containing new structures.
	"""
    index1 = 0
    pop = []
    for i in range(Optimizer.nindiv):
        if Optimizer.structure == 'Defect':
            individ = get_defect_indiv(Optimizer)
        elif Optimizer.structure == 'Surface':
            individ = get_surface_indiv(Optimizer)
        elif Optimizer.structure == 'Crystal':
            individ = get_crystal_indiv(Optimizer)
        else:
            if 'sphere' in Optimizer.generate_flag:
                ind = gen_pop_sphere(Optimizer.atomlist, Optimizer.size)
            else:
                ind = gen_pop_box(Optimizer.atomlist, Optimizer.size)
            individ = Individual(ind)
        individ.index = index1
        if Optimizer.genealogy:
            individ.history_index = repr(index1)
        Optimizer.output.write('Generated cluster individual with natoms = ' +
                               repr(individ[0].get_number_of_atoms()) + '\n')
        pop.append(individ)
        index1 = index1 + 1
    # Generate new atomlist concentrations based on cluster+box
    if Optimizer.structure == 'Defect':
        if Optimizer.alloy:
            concents = []
            for ind in pop:
                cs = []
                for sym, c, u, m in Optimizer.atomlist:
                    sylen = [atm for atm in ind[0] if atm.symbol == sym]
                    cs.append(len(sylen))
                concents.append(cs)
            natmlist = [0] * len(Optimizer.atomlist)
            for i in range(len(concents[0])):
                alls = [cs[i] for cs in concents]
                avgall = int(sum(alls) / len(alls))
                if avgall >= Optimizer.atomlist[i][1]:
                    natmlist[i] = (Optimizer.atomlist[i][0], avgall,
                                   Optimizer.atomlist[i][2],
                                   Optimizer.atomlist[i][3])
                else:
                    natmlist[i] = (Optimizer.atomlist[i][0],
                                   Optimizer.atomlist[i][1],
                                   Optimizer.atomlist[i][2],
                                   Optimizer.atomlist[i][3])
        else:
            natmlist = [0] * len(Optimizer.atomlist)
            for i in range(len(Optimizer.atomlist)):
                atms1 = [
                    inds for inds in pop[0][0]
                    if inds.symbol == Optimizer.atomlist[i][0]
                ]
                natmlist[i] = (Optimizer.atomlist[i][0], len(atms1),
                               Optimizer.atomlist[i][2],
                               Optimizer.atomlist[i][3])
        Optimizer.atomlist = natmlist
        Optimizer.output.write(
            '\n\nNew atomlist concentrations based on cluster+box = ' +
            repr(Optimizer.atomlist) + '\n')
    return pop
예제 #4
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def read_individual(indivfile, n=-1):
    """Function to write the data of an individual class object to a flat file
    Input:
        indivfile = String or fileobject for file to be read from
        n = which individual from file to return. Default is last individual written.
            optional All
    Output:
        returns an individual class object or list of individual class objects depending on value of n
    """
    if isinstance(indivfile, str):
        indivfile=open(indivfile, 'r')
    all_lines = indivfile.readlines()
    indivfile.close()
    linen = 0
    all_indivs = []
    while linen < len(all_lines):
        if '----------' in all_lines[linen]:
            individ = Individual(Atoms())
        elif 'Structure information' in all_lines[linen]:
            natomstruct = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natomstruct):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ = Individual(atomstruct)
            linen += 2+natomstruct
        elif 'structure cell' in all_lines[linen]:
            cell_line = all_lines[linen].split('=')
            structcell = eval(cell_line[1])
            individ[0].set_cell(structcell)
        elif 'fitness' in all_lines[linen]:
            fitline = all_lines[linen].split('=')
            individ.fitness = float(fitline[1])
        elif 'history_index' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.history_index = line[1].strip()
        elif 'index' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.index = float(line[1])
        elif 'tenergymx' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.tenergymx = float(line[1])
        elif 'tenergymin' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.tenergymin = float(line[1])
        elif 'energy' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.energy = float(line[1])
        elif 'pressure' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.pressure = float(line[1])
        elif 'volume' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.volume = float(line[1])
        elif 'force' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.force = float(line[1])
        elif 'purebulkenpa' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.purebulkenpa = float(line[1])
        elif 'natomsbulk' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.natomsbulk = float(line[1])
        elif 'fingerprint' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.fingerprint = eval(line[1])
        elif 'swpalist' in all_lines[linen]:
            line = all_lines[linen].split('=')
            individ.swaplist = eval(line[1])
        elif 'bulki cell' in all_lines[linen]:
            line = all_lines[linen].split('=')
            cell = eval(line[1])
            individ.bulki.set_cell(cell)
        elif 'bulki' in all_lines[linen]:
            natoms = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natoms):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ.bulki = atomstruct.copy()
            linen += 2+natoms
        elif 'bulko cell' in all_lines[linen]:
            line = all_lines[linen].split('=')
            cell = eval(line[1])
            individ.bulko.set_cell(cell)
        elif 'bulko' in all_lines[linen]:
            natoms = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natoms):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ.bulko = atomstruct.copy()
            linen += 2+natoms
        elif 'box cell' in all_lines[linen]:
            line = all_lines[linen].split('=')
            cell = eval(line[1])
            individ.box.set_cell(cell)
        elif 'box' in all_lines[linen]:
            natoms = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natoms):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ.box = atomstruct.copy()
            linen += 2+natoms
        elif 'vacancies cell' in all_lines[linen]:
            line = all_lines[linen].split('=')
            cell = eval(line[1])
            individ.vacancies.set_cell(cell)
        elif 'vacancies' in all_lines[linen]:
            natoms = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natoms):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ.vacancies = atomstruct.copy()
            linen += 2+natoms
        elif 'swaps cell' in all_lines[linen]:
            line = all_lines[linen].split('=')
            cell = eval(line[1])
            individ.swaps.set_cell(cell)
        elif 'swaps' in all_lines[linen]:
            natoms = int(all_lines[linen+1])
            atomstruct = Atoms()
            for i in range(natoms):
                a = all_lines[linen+i+3].split()
                sym = a[0]
                position = [float(a[1]),float(a[2]),float(a[3])]
                atomstruct.append(Atom(symbol=sym,position=position))
            individ.swaps = atomstruct.copy()
            linen += 2+natoms
        elif 'Finish' in all_lines[linen]:
            all_indivs.append(individ.duplicate())
        linen+=1
    if n=='All':
        return all_indivs
    else:
        return all_indivs[n]
예제 #5
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         Optimizer.output.flush()
         Optimizer.nindiv -= 1
     if successflag:
         Optimizer.output.write(
             'Found good individual = {0}\n'.format(indiv))
         if Optimizer.structure == 'Defect':
             individ = get_defect_restart_indiv(Optimizer, indiv)
         elif Optimizer.structure == 'Surface':
             individ = get_surface_restart_indiv(Optimizer, indiv)
         else:
             cell = indiv.get_cell()
             if cell[0][0] == 1.0:
                 indiv.set_cell(
                     [Optimizer.size, Optimizer.size, Optimizer.size])
             individ = Individual(indiv)
         individ.index = index1
         if Optimizer.genealogy:
             individ.history_index = repr(index1)
         pop.append(individ)
         index1 = index1 + 1
 if len(pop) == 0:
     raise RuntimeError('Unable to load any structures for Restart')
 # Generate new atomlist concentrations based on cluster+box
 if Optimizer.structure == 'Defect':
     if Optimizer.alloy:
         concents = []
         for ind in pop:
             cs = []
             for sym, c, u, m in Optimizer.atomlist:
                 sylen = [atm for atm in ind[0] if atm.symbol == sym]
                 cs.append(len(sylen))