def cell_relax_lammps(indiv, Optimizer): """Move function to perform Lammps box/relax for cell. Intended for use in Crystal Optimization Inputs: indiv = Individual class object to be altered Optimizer = Optimizer class object with needed parameters Outputs: indiv = Altered Individual class object """ if 'MU' in Optimizer.debug: debug = True else: debug = False cwd1=os.getcwd() Optimizer.output.write('LAMMPS fix box/relax performed\n') parameters=copy.deepcopy(Optimizer.calc.parameters) passflag=True try: parameters['mass'][len(parameters['mass'])-1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: try: parameters['pair_coeff'][0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: print 'WARNING: LAMMPS Cell relax move trouble with potential. SKIPPING' Optimizer.output.write('WARNING: Minimizer quit. LAMMPS Cell relax move trouble with potential - Box relaxation unsuccessful\n') passflag=False if passflag: filesL = [ Optimizer.pot_file ] if Optimizer.lammps_keep_files: rank = 0 path = os.path.join(os.getcwd(),'{0}-rank{1}'.format(Optimizer.filename,rank)) if not os.path.exists(os.path.join(path,'LAMMPSFiles')): os.mkdir(os.path.join(path,'LAMMPSFiles')) real_rank = MPI.COMM_WORLD.Get_rank() tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'),'rank-{0}'.format(real_rank)) # calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/') calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=tmpdir) else: calc2 = LAMMPS(parameters=parameters, files=filesL) atmsdup=indiv[0].copy() atmsdup.set_calculator(calc2) try: OUT=atmsdup.calc.calculate(atmsdup) indiv[0].set_cell(OUT['atoms'].get_cell()) indiv[0].set_positions(OUT['atoms'].get_positions()) Optimizer.output.write('Energy = '+repr(OUT['thermo'][-1]['pe']/indiv[0].get_number_of_atoms())+'\n') except: Optimizer.output.write('WARNING: Minimizer quit - Box relaxation unsuccessful\n') #pdb.set_trace() os.chdir(cwd1) calc2.clean() Optimizer.output.write(repr(indiv[0].get_cell())+'\n') muttype='LBR' if indiv.energy==0: indiv.history_index=indiv.history_index+'m'+muttype else: indiv.history_index=repr(indiv.index)+'m'+muttype return indiv
def cell_relax_lammps(indiv, Optimizer): """Move function to perform Lammps box/relax for cell. Intended for use in Crystal Optimization Inputs: indiv = Individual class object to be altered Optimizer = Optimizer class object with needed parameters Outputs: indiv = Altered Individual class object """ if 'MU' in Optimizer.debug: debug = True else: debug = False cwd1=os.getcwd() Optimizer.output.write('LAMMPS fix box/relax performed\n') parameters=copy.deepcopy(Optimizer.calc.parameters) passflag=True try: parameters['mass'][len(parameters['mass'])-1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: try: parameters['pair_coeff'][0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: print 'WARNING: LAMMPS Cell relax move trouble with potential. SKIPPING' Optimizer.output.write('WARNING: Minimizer quit. LAMMPS Cell relax move trouble with potential - Box relaxation unsuccessful\n') passflag=False if passflag: filesL = [ Optimizer.pot_file ] if Optimizer.lammps_keep_files: calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/') else: calc2 = LAMMPS(parameters=parameters, files=filesL) atmsdup=indiv[0].copy() atmsdup.set_calculator(calc2) try: OUT=atmsdup.calc.calculate(atmsdup) indiv[0].set_cell(OUT['atoms'].get_cell()) indiv[0].set_positions(OUT['atoms'].get_positions()) Optimizer.output.write('Energy = '+repr(OUT['thermo'][-1]['pe']/indiv[0].get_number_of_atoms())+'\n') except: Optimizer.output.write('WARNING: Minimizer quit - Box relaxation unsuccessful\n') #pdb.set_trace() os.chdir(cwd1) calc2.clean() Optimizer.output.write(repr(indiv[0].get_cell())+'\n') muttype='LBR' if indiv.energy==0: indiv.history_index=indiv.history_index+'m'+muttype else: indiv.history_index=repr(indiv.index)+'m'+muttype return indiv
def eval_energy(Optimizer, individ): """Function to evaluate energy of an individual Inputs: input = [Optimizer class object with parameters, Individual class structure to be evaluated] Outputs: energy, bul, individ, signal energy = energy of Individual evaluated bul = bulk structure of Individual if simulation structure is Defect individ = Individual class structure evaluated signal = string of information about evaluation """ #logger = initialize_logger(Optimizer.loggername) logger = logging.getLogger(Optimizer.loggername) if 'MAST' in Optimizer.calc_method: energy = individ.energy bul = individ.bulki signal = 'Received MAST structure\n' logger.info( 'Received individual index = {0} from MAST with energy {1}. Returning with no evaluation' .format(individ.index, individ.energy)) else: if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank() logger.info( 'Received individual HI = {0} with energy {1} for energy evaluation' .format(individ.history_index, individ.energy)) STR = '----Individual ' + str( individ.history_index) + ' Optimization----\n' indiv = individ[0] if 'EE' in Optimizer.debug: debug = True else: debug = False if debug: write_xyz(Optimizer.debugfile, indiv, 'Received by eval_energy') Optimizer.debugfile.flush() logger.debug('Writing recieved individual to debug file') # Establish individual structure for evaluation. Piece together regions when necessary. if Optimizer.structure == 'Defect': indi = indiv.copy() bulk = individ.bulki nat = indi.get_number_of_atoms() if debug: logger.info( 'Extending defect structure to include bulk len(r1+r2)={0} len(bulk)={1}' .format(nat, len(bulk))) csize = bulk.get_cell() totalsol = Atoms(cell=csize, pbc=True) totalsol.extend(indi) totalsol.extend(bulk) for sym, c, m, u in Optimizer.atomlist: nc = len([atm for atm in totalsol if atm.symbol == sym]) STR += 'Defect configuration contains ' + repr( nc) + ' ' + repr(sym) + ' atoms\n' elif Optimizer.structure == 'Surface': totalsol = Atoms() totalsol.extend(indiv) nat = indiv.get_number_of_atoms() totalsol.extend(individ.bulki) if debug: logger.info( 'Extending surface structure to include bulk len(r1+r2)={0} len(bulk)={1}' .format(nat, len(individ.bulki))) for sym, c, m, u in Optimizer.atomlist: nc = len([atm for atm in totalsol if atm.symbol == sym]) STR += 'Surface-Bulk configuration contains ' + repr( nc) + ' ' + repr(sym) + ' atoms\n' cell = numpy.maximum.reduce(indiv.get_cell()) totalsol.set_cell([cell[0], cell[1], 500]) totalsol.set_pbc([True, True, False]) elif Optimizer.structure == 'Cluster': totalsol = indiv.copy() nat = len(totalsol) if debug: logger.info( 'Extending cluster with {0} atoms to center of evaluation box of size {1}' .format(nat, Optimizer.large_box_size)) origcell = indiv.get_cell() totalsol.set_cell([ Optimizer.large_box_size, Optimizer.large_box_size, Optimizer.large_box_size ]) totalsol.translate([ Optimizer.large_box_size / 2.0, Optimizer.large_box_size / 2.0, Optimizer.large_box_size / 2.0 ]) elif Optimizer.structure == 'Crystal': totalsol = indiv.copy() nat = len(totalsol) else: print 'WARNING: In EvalEnergy. Optimizer.structure not recognized' logger.warning('Optimizer.structure not recognized') # Check for atoms that are too close or out of constrained location if Optimizer.constrain_position: if Optimizer.structure == 'Defect': if debug: logger.info('Constraining positions of defect') totalsol, stro = constrain_positions(totalsol, Optimizer.solidbulk, Optimizer.sf) if debug: logger.info(stro) STR += str0 min_len = 0.7 if not Optimizer.fixed_region: if debug: logger.info('Running check minimum distance') totalsol, STR = check_min_dist(totalsol, Optimizer.structure, nat, min_len, STR) if debug: write_xyz(Optimizer.debugfile, totalsol, 'After minlength check') Optimizer.debugfile.flush() logger.debug( 'Writing individual after checking minimum length') # Set calculator to use to get forces/energies if Optimizer.parallel: calc = setup_calculator(Optimizer) if Optimizer.fixed_region: if debug: logger.info('Setting up fixed region calculator') pms = copy.deepcopy(calc.parameters) try: pms['mass'][ len(pms['mass']) - 1] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format( nat) except KeyError: pms['pair_coeff'][ 0] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format( nat) calc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir) lmin = copy.copy(Optimizer.lammps_min) if debug: logger.info('Setting up no local minimization calculator') Optimizer.lammps_min = None Optimizer.static_calc = setup_calculator(Optimizer) Optimizer.lammps_min = lmin else: calc = Optimizer.calc totalsol.set_calculator(calc) totalsol.set_pbc(True) # Perform Energy Minimization if not Optimizer.parallel: if debug: write_xyz(Optimizer.debugfile, totalsol, 'Individual sent to Energy Minimizer') logger.debug('Writing structure sent to energy minimizer') try: cwd = os.getcwd() if Optimizer.ase_min == True: if debug: logger.info('Running ASE minimizer') if Optimizer.calc_method == 'LennardJones': logger.warn('Must run ase LJ calculator with pbc=False') totalsol.set_pbc(False) totalsol, energy, pressure, volume, STR = run_ase_min( totalsol, Optimizer.ase_min_fmax, Optimizer.ase_min_maxsteps, Optimizer.fitness_scheme, STR) else: if debug: logger.info('Running local energy calculator') if Optimizer.fixed_region: totalsol, energy, pressure, volume, STR = run_energy_eval( totalsol, Optimizer.calc_method, Optimizer.fixed_region, Optimizer.fitness_scheme, STR, Optimizer.static_calc) else: totalsol, energy, pressure, volume, STR = run_energy_eval( totalsol, Optimizer.calc_method, False, Optimizer.fitness_scheme, STR) except Exception, e: logger.critical('Error in energy evaluation: {0}'.format(e), exc_info=True) path = os.path.join(cwd, 'TroubledLammps') if not os.path.exists(path): os.mkdir(path) #Copy files over shutil.copyfile( calc.trajfile, os.path.join(path, os.path.basename(calc.trajfile))) shutil.copyfile(calc.infile, os.path.join(path, os.path.basename(calc.infile))) shutil.copyfile(calc.logfile, os.path.join(path, os.path.basename(calc.logfile))) shutil.copyfile( calc.datafile, os.path.join(path, os.path.basename(calc.datafile))) raise RuntimeError('{0}:{1}'.format(Exception, e)) if not Optimizer.parallel: if debug: write_xyz(Optimizer.debugfile, totalsol, 'Individual after Energy Minimization') Optimizer.debugfile.flush() logger.debug( 'Writing structure recieved from energy minimizer') # Separate structures into distinct pieces if Optimizer.structure == 'Defect': if Optimizer.fixed_region == True or Optimizer.finddefects == False: if debug: logger.info( 'Identifying atoms in defect structure based on ID') individ[0] = totalsol[0:nat] bul = totalsol[(nat):len(totalsol)] individ[0].set_cell(csize) else: if debug: logger.info( 'Applying find defects scheme to identify R1 and R2 for Defect' ) if 'FD' in Optimizer.debug: outt = find_defects(totalsol, Optimizer.solidbulk, Optimizer.sf, atomlistcheck=Optimizer.atomlist, trackvacs=Optimizer.trackvacs, trackswaps=Optimizer.trackswaps, debug=Optimizer.debugfile) else: outt = find_defects(totalsol, Optimizer.solidbulk, Optimizer.sf, atomlistcheck=Optimizer.atomlist, trackvacs=Optimizer.trackvacs, trackswaps=Optimizer.trackswaps, debug=False) individ[0] = outt[0] bul = outt[1] individ.vacancies = outt[2] individ.swaps = outt[3] STR += outt[4] indiv = individ[0] elif Optimizer.structure == 'Surface': if debug: logger.info('Finding surface top layer') top, bul = find_top_layer(totalsol, Optimizer.surftopthick) indiv = top.copy() individ[0] = top.copy() bul = Atoms() elif Optimizer.structure == 'Crystal': if debug: logger.info('Checking crystal cell type') celltype = check_cell_type(totalsol) STR += 'Cell structure = {0}\n'.format(celltype) bul = Atoms() individ[0] = totalsol.copy() elif Optimizer.structure == 'Cluster': volume = get_cluster_volume(totalsol) bul = Atoms() if debug: logger.info( 'Translating cluster back to smaller box size location') totalsol.translate([ -Optimizer.large_box_size / 2.0, -Optimizer.large_box_size / 2.0, -Optimizer.large_box_size / 2.0 ]) totalsol.set_cell(origcell) individ[0] = totalsol.copy() # Add concentration energy dependence if Optimizer.forcing == 'energy_bias': if debug: logger.info( 'Applying energy bias for atoms with different number of atoms of type than in atomlist' ) n = [0] * len(Optimizer.atomlist) for i in range(len(Optimizer.atomlist)): n[i] = len([ inds for inds in totalsol if inds.symbol == Optimizer.atomlist[i][0] ]) n[i] = abs(n[i] - Optimizer.atomlist[i][1]) factor = sum(n)**3 energy = (energy + factor) / totalsol.get_number_of_atoms() STR += 'Energy with Bias = {0}\n'.format(energy) elif Optimizer.forcing == 'chem_pot': if debug: logger.info( 'Applying chemical potential bias for atoms with different number of atoms of type than in atomlist' ) n = [0] * len(Optimizer.atomlist) for i in range(len(Optimizer.atomlist)): n[i] = len([ inds for inds in totalsol if inds.symbol == Optimizer.atomlist[i][0] ]) n[i] = n[i] * Optimizer.atomlist[i][3] factor = sum(n) energy = (energy + factor) / totalsol.get_number_of_atoms() STR += 'Energy with Chemical Potential = {0}\n'.format(energy) individ.energy = energy individ.buli = bul individ.pressure = pressure individ.volume = volume if Optimizer.fingerprinting: if debug: logger.info('Identifying fingerprint of new structure') individ.fingerprint = get_fingerprint(Optimizer, individ, Optimizer.fpbin, Optimizer.fpcutoff) if Optimizer.parallel: calc.clean() signal = 'Evaluated individual {0} on {1}\n'.format( individ.index, rank) signal += STR else: signal = STR
def eval_energy(Optimizer, individ): """Function to evaluate energy of an individual Inputs: input = [Optimizer class object with parameters, Individual class structure to be evaluated] Outputs: energy, bul, individ, signal energy = energy of Individual evaluated bul = bulk structure of Individual if simulation structure is Defect individ = Individual class structure evaluated signal = string of information about evaluation """ #logger = initialize_logger(Optimizer.loggername) logger = logging.getLogger(Optimizer.loggername) if 'MAST' in Optimizer.calc_method: energy = individ.energy bul = individ.bulki signal = 'Received MAST structure\n' logger.info('Received individual index = {0} from MAST with energy {1}. Returning with no evaluation'.format( individ.index, individ.energy)) else: if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank() logger.info('Received individual HI = {0} with energy {1} for energy evaluation'.format( individ.history_index, individ.energy)) STR='----Individual ' + str(individ.history_index)+ ' Optimization----\n' indiv=individ[0] if 'EE' in Optimizer.debug: debug = True else: debug = False if debug: write_xyz(Optimizer.debugfile,indiv,'Received by eval_energy') Optimizer.debugfile.flush() logger.debug('Writing recieved individual to debug file') # Establish individual structure for evaluation. Piece together regions when necessary. if Optimizer.structure=='Defect': indi=indiv.copy() bulk=individ.bulki nat=indi.get_number_of_atoms() if debug: logger.info('Extending defect structure to include bulk len(r1+r2)={0} len(bulk)={1}'.format(nat,len(bulk))) csize=bulk.get_cell() totalsol=Atoms(cell=csize, pbc=True) totalsol.extend(indi) totalsol.extend(bulk) for sym,c,m,u in Optimizer.atomlist: nc=len([atm for atm in totalsol if atm.symbol==sym]) STR+='Defect configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n' elif Optimizer.structure=='Surface': totalsol=Atoms() totalsol.extend(indiv) nat=indiv.get_number_of_atoms() totalsol.extend(individ.bulki) if debug: logger.info('Extending surface structure to include bulk len(r1+r2)={0} len(bulk)={1}'.format(nat,len(individ.bulki))) for sym,c,m,u in Optimizer.atomlist: nc=len([atm for atm in totalsol if atm.symbol==sym]) STR+='Surface-Bulk configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n' cell=numpy.maximum.reduce(indiv.get_cell()) totalsol.set_cell([cell[0],cell[1],500]) totalsol.set_pbc([True,True,False]) elif Optimizer.structure=='Cluster': totalsol = indiv.copy() nat = len(totalsol) if debug: logger.info('Extending cluster with {0} atoms to center of evaluation box of size {1}'.format(nat,Optimizer.large_box_size)) origcell = indiv.get_cell() totalsol.set_cell([Optimizer.large_box_size,Optimizer.large_box_size,Optimizer.large_box_size]) totalsol.translate([Optimizer.large_box_size/2.0,Optimizer.large_box_size/2.0,Optimizer.large_box_size/2.0]) elif Optimizer.structure=='Crystal': totalsol = indiv.copy() nat = len(totalsol) else: print 'WARNING: In EvalEnergy. Optimizer.structure not recognized' logger.warning('Optimizer.structure not recognized') # Check for atoms that are too close or out of constrained location if Optimizer.constrain_position: if Optimizer.structure=='Defect': if debug: logger.info('Constraining positions of defect') totalsol, stro = constrain_positions(totalsol, Optimizer.solidbulk, Optimizer.sf) if debug: logger.info(stro) STR+=str0 min_len=0.7 if not Optimizer.fixed_region: if debug: logger.info('Running check minimum distance') totalsol, STR = check_min_dist(totalsol, Optimizer.structure, nat, min_len, STR) if debug: write_xyz(Optimizer.debugfile,totalsol,'After minlength check') Optimizer.debugfile.flush() logger.debug('Writing individual after checking minimum length') # Set calculator to use to get forces/energies if Optimizer.parallel: calc = setup_calculator(Optimizer) if Optimizer.fixed_region: if debug: logger.info('Setting up fixed region calculator') pms=copy.deepcopy(calc.parameters) try: pms['mass'][len(pms['mass'])-1] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(nat) except KeyError: pms['pair_coeff'][0] += '\ngroup RO id >= {0}\nfix freeze RO setforce 0.0 0.0 0.0\n'.format(nat) calc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir) lmin = copy.copy(Optimizer.lammps_min) if debug: logger.info('Setting up no local minimization calculator') Optimizer.lammps_min = None Optimizer.static_calc = setup_calculator(Optimizer) Optimizer.lammps_min = lmin else: calc=Optimizer.calc totalsol.set_calculator(calc) totalsol.set_pbc(True) # Perform Energy Minimization if not Optimizer.parallel: if debug: write_xyz(Optimizer.debugfile,totalsol,'Individual sent to Energy Minimizer') logger.debug('Writing structure sent to energy minimizer') try: cwd = os.getcwd() if Optimizer.ase_min == True: if debug: logger.info('Running ASE minimizer') if Optimizer.calc_method=='LennardJones': logger.warn('Must run ase LJ calculator with pbc=False') totalsol.set_pbc(False) totalsol, energy, pressure, volume, STR = run_ase_min(totalsol, Optimizer.ase_min_fmax, Optimizer.ase_min_maxsteps, Optimizer.fitness_scheme, STR) else: if debug: logger.info('Running local energy calculator') if Optimizer.fixed_region: totalsol, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, Optimizer.fixed_region, Optimizer.fitness_scheme, STR, Optimizer.static_calc) else: totalsol, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, False, Optimizer.fitness_scheme, STR) except Exception, e: logger.critical('Error in energy evaluation: {0}'.format(e), exc_info=True) path = os.path.join(cwd,'TroubledLammps') if not os.path.exists(path): os.mkdir(path) #Copy files over shutil.copyfile(calc.trajfile,os.path.join(path,os.path.basename(calc.trajfile))) shutil.copyfile(calc.infile,os.path.join(path,os.path.basename(calc.infile))) shutil.copyfile(calc.logfile,os.path.join(path,os.path.basename(calc.logfile))) shutil.copyfile(calc.datafile,os.path.join(path,os.path.basename(calc.datafile))) raise RuntimeError('{0}:{1}'.format(Exception,e)) if not Optimizer.parallel: if debug: write_xyz(Optimizer.debugfile,totalsol,'Individual after Energy Minimization') Optimizer.debugfile.flush() logger.debug('Writing structure recieved from energy minimizer') # Separate structures into distinct pieces if Optimizer.structure=='Defect': if Optimizer.fixed_region==True or Optimizer.finddefects==False: if debug: logger.info('Identifying atoms in defect structure based on ID') individ[0]=totalsol[0:nat] bul=totalsol[(nat):len(totalsol)] individ[0].set_cell(csize) else: if debug: logger.info('Applying find defects scheme to identify R1 and R2 for Defect') if 'FD' in Optimizer.debug: outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=Optimizer.debugfile) else: outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False) individ[0]=outt[0] bul=outt[1] individ.vacancies = outt[2] individ.swaps = outt[3] STR += outt[4] indiv=individ[0] elif Optimizer.structure=='Surface': if debug: logger.info('Finding surface top layer') top,bul=find_top_layer(totalsol,Optimizer.surftopthick) indiv=top.copy() individ[0]=top.copy() bul = Atoms() elif Optimizer.structure=='Crystal': if debug: logger.info('Checking crystal cell type') celltype = check_cell_type(totalsol) STR+='Cell structure = {0}\n'.format(celltype) bul = Atoms() individ[0] = totalsol.copy() elif Optimizer.structure=='Cluster': volume = get_cluster_volume(totalsol) bul = Atoms() if debug: logger.info('Translating cluster back to smaller box size location') totalsol.translate([-Optimizer.large_box_size/2.0,-Optimizer.large_box_size/2.0,-Optimizer.large_box_size/2.0]) totalsol.set_cell(origcell) individ[0] = totalsol.copy() # Add concentration energy dependence if Optimizer.forcing=='energy_bias': if debug: logger.info('Applying energy bias for atoms with different number of atoms of type than in atomlist') n=[0]*len(Optimizer.atomlist) for i in range(len(Optimizer.atomlist)): n[i]=len([inds for inds in totalsol if inds.symbol==Optimizer.atomlist[i][0]]) n[i]=abs(n[i]-Optimizer.atomlist[i][1]) factor=sum(n)**3 energy=(energy+factor)/totalsol.get_number_of_atoms() STR+='Energy with Bias = {0}\n'.format(energy) elif Optimizer.forcing=='chem_pot': if debug: logger.info('Applying chemical potential bias for atoms with different number of atoms of type than in atomlist') n=[0]*len(Optimizer.atomlist) for i in range(len(Optimizer.atomlist)): n[i]=len([inds for inds in totalsol if inds.symbol==Optimizer.atomlist[i][0]]) n[i]=n[i]*Optimizer.atomlist[i][3] factor=sum(n) energy=(energy+factor)/totalsol.get_number_of_atoms() STR+='Energy with Chemical Potential = {0}\n'.format(energy) individ.energy=energy individ.buli=bul individ.pressure=pressure individ.volume=volume if Optimizer.fingerprinting: if debug: logger.info('Identifying fingerprint of new structure') individ.fingerprint=get_fingerprint(Optimizer,individ,Optimizer.fpbin,Optimizer.fpcutoff) if Optimizer.parallel: calc.clean() signal = 'Evaluated individual {0} on {1}\n'.format(individ.index,rank) signal +=STR else: signal=STR
def cell_shape(indiv, Optimizer): """Move function to forcefully alter the unit cell shape Inputs: indiv = Individual class object to be altered Optimizer = Optimizer class object with needed parameters Outputs: indiv = Altered Individual class object """ if 'MU' in Optimizer.debug: debug = True else: debug = False Optimizer.output.write('Cell Shape change mutation\n') Optimizer.output.write('Index = ' + repr(indiv.index) + '\n') structure = random.choice(Optimizer.cell_shape_options) cello = indiv[0].get_cell() if structure == 'cubic': #Set to cubic shape an, bn, cn = [numpy.linalg.norm(v) for v in cello] a = (an + bn + cn) / 3.0 celln = numpy.array([[a, 0, 0], [0, a, 0], [0, 0, a]]) Optimizer.output.write('Mutating to cubic\n') muttype = 'CSC' elif structure == 'hexagonal': #Set to hexagonal shape an, bn, cn = [numpy.linalg.norm(v) for v in cello] a = (an + bn) / 2.0 c = cn if c <= a: c = random.uniform(a + 1, 10) trans = numpy.array([[1, 0, 0], [-0.5, (3.0**0.5) / 2.0, 0], [0, 0, 1]]) trans[0] = [a * i for i in trans[0]] trans[1] = [a * i for i in trans[1]] trans[2] = [c * i for i in trans[2]] celln = trans Optimizer.output.write('Mutating to Hexagonal\n') muttype = 'CSH' elif structure == 'tetragonal': #Set to tetragonal shape an, bn, cn = [numpy.linalg.norm(v) for v in cello] a = (an + bn) / 2.0 c = cn if c == a: c = random.uniform(1, 10) celln = numpy.array([[a, 0, 0], [0, a, 0], [0, 0, c]]) Optimizer.output.write('Mutating to tetragonal\n') muttype = 'CSTe' elif structure == 'orthorhombic': #Set to orthorhombic a = random.uniform(2, 10) b = random.uniform(2, 10) c = random.uniform(2, 10) celln = numpy.array([[a, 0, 0], [0, b, 0], [0, 0, c]]) Optimizer.output.write('Mutating to orthorhombic\n') muttype = 'CSO' elif structure == 'monoclinic': #Set to monoclinic a, b, c = [numpy.linalg.norm(v) for v in cello] if a == b: b = random.uniform(1, 10) trans = numpy.array([(1 + random.random()) * c, 0, (1 + random.random()) * c]) celln = numpy.array([[a, 0, 0], [0, b, 0], [0, 0, 0]]) celln[2] = trans Optimizer.output.write('Mutating to monoclinic\n') muttype = 'CSM' elif structure == 'triclinic': #Set to triclinic a, b, c = [numpy.linalg.norm(v) for v in cello] celln = numpy.array([[a, 0, 0], [(1 + random.random()) * b, (1 + random.random()) * b, 0], [(1 + random.random()) * c, 0, (1 + random.random()) * c]]) Optimizer.output.write('Mutating to triclinic\n') muttype = 'CSTr' indiv[0].set_cell(celln) #Relax new box shape with Lammps box/reax for cell Optimizer.output.write('LAMMPS fix box/relax performed\n') cwd1 = os.getcwd() parameters = copy.deepcopy(Optimizer.calc.parameters) try: parameters['mass'][len(parameters['mass']) - 1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: parameters['pair_coeff'][ 0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' filesL = [Optimizer.pot_file] if Optimizer.lammps_keep_files: calc2 = LAMMPS(parameters=parameters, files=filesL, keep_tmp_files=True, tmp_dir=os.getcwd() + '/' + Optimizer.filename + '/Lammpsrun2/') else: calc2 = LAMMPS(parameters=parameters, files=filesL) atmsdup = indiv[0].copy() atmsdup.set_calculator(calc2) try: OUT = atmsdup.calc.calculate(atmsdup) indiv[0].set_cell(OUT['atoms'].get_cell()) indiv[0].set_positions(OUT['atoms'].get_positions()) Optimizer.output.write('Energy = ' + repr(OUT['thermo'][-1]['pe'] / indiv[0].get_number_of_atoms()) + '\n') except: Optimizer.output.write( 'WARNING: Minimizer quit - Box relaxation unsuccessful\n') #pdb.set_trace() os.chdir(cwd1) calc2.clean() Optimizer.output.write(repr(indiv[0].get_cell()) + '\n') if indiv.energy == 0: indiv.history_index = indiv.history_index + 'm' + muttype else: indiv.history_index = repr(indiv.index) + 'm' + muttype return indiv
def cell_shape(indiv, Optimizer): """Move function to forcefully alter the unit cell shape Inputs: indiv = Individual class object to be altered Optimizer = Optimizer class object with needed parameters Outputs: indiv = Altered Individual class object """ if 'MU' in Optimizer.debug: debug = True else: debug = False Optimizer.output.write('Cell Shape change mutation\n') Optimizer.output.write('Index = '+repr(indiv.index)+'\n') structure=random.choice(Optimizer.cell_shape_options) cello=indiv[0].get_cell() if structure=='cubic': #Set to cubic shape an,bn,cn = [numpy.linalg.norm(v) for v in cello] a=(an+bn+cn)/3.0 celln=numpy.array([[a,0,0],[0,a,0],[0,0,a]]) Optimizer.output.write('Mutating to cubic\n') muttype='CSC' elif structure=='hexagonal': #Set to hexagonal shape an,bn,cn = [numpy.linalg.norm(v) for v in cello] a=(an+bn)/2.0 c=cn if c<=a: c=random.uniform(a+1,10) trans=numpy.array([[1,0,0],[-0.5,(3.0**0.5)/2.0,0],[0,0,1]]) trans[0]=[a*i for i in trans[0]] trans[1]=[a*i for i in trans[1]] trans[2]=[c*i for i in trans[2]] celln=trans Optimizer.output.write('Mutating to Hexagonal\n') muttype='CSH' elif structure=='tetragonal': #Set to tetragonal shape an,bn,cn = [numpy.linalg.norm(v) for v in cello] a=(an+bn)/2.0 c=cn if c==a: c=random.uniform(1,10) celln=numpy.array([[a,0,0],[0,a,0],[0,0,c]]) Optimizer.output.write('Mutating to tetragonal\n') muttype='CSTe' elif structure=='orthorhombic': #Set to orthorhombic a=random.uniform(2,10) b=random.uniform(2,10) c=random.uniform(2,10) celln=numpy.array([[a,0,0],[0,b,0],[0,0,c]]) Optimizer.output.write('Mutating to orthorhombic\n') muttype='CSO' elif structure=='monoclinic': #Set to monoclinic a,b,c = [numpy.linalg.norm(v) for v in cello] if a==b: b=random.uniform(1,10) trans=numpy.array([(1+random.random())*c, 0, (1+random.random())*c]) celln=numpy.array([[a,0,0],[0,b,0],[0,0,0]]) celln[2]=trans Optimizer.output.write('Mutating to monoclinic\n') muttype='CSM' elif structure=='triclinic': #Set to triclinic a,b,c = [numpy.linalg.norm(v) for v in cello] celln=numpy.array([[a,0,0],[(1+random.random())*b,(1+random.random())*b,0],[(1+random.random())*c,0,(1+random.random())*c]]) Optimizer.output.write('Mutating to triclinic\n') muttype='CSTr' indiv[0].set_cell(celln) #Relax new box shape with Lammps box/reax for cell Optimizer.output.write('LAMMPS fix box/relax performed\n') cwd1=os.getcwd() parameters=copy.deepcopy(Optimizer.calc.parameters) try: parameters['mass'][len(parameters['mass'])-1] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' except KeyError: parameters['pair_coeff'][0] += '\nfix 1 all box/relax iso 0.0 vmax 0.001' filesL = [ Optimizer.pot_file ] if Optimizer.lammps_keep_files: calc2 = LAMMPS(parameters=parameters, files=filesL,keep_tmp_files=True, tmp_dir=os.getcwd()+'/'+Optimizer.filename+'/Lammpsrun2/') else: calc2 = LAMMPS(parameters=parameters, files=filesL) atmsdup=indiv[0].copy() atmsdup.set_calculator(calc2) try: OUT=atmsdup.calc.calculate(atmsdup) indiv[0].set_cell(OUT['atoms'].get_cell()) indiv[0].set_positions(OUT['atoms'].get_positions()) Optimizer.output.write('Energy = '+repr(OUT['thermo'][-1]['pe']/indiv[0].get_number_of_atoms())+'\n') except: Optimizer.output.write('WARNING: Minimizer quit - Box relaxation unsuccessful\n') #pdb.set_trace() os.chdir(cwd1) calc2.clean() Optimizer.output.write(repr(indiv[0].get_cell())+'\n') if indiv.energy==0: indiv.history_index=indiv.history_index+'m'+muttype else: indiv.history_index=repr(indiv.index)+'m'+muttype return indiv