def setup_fixed_region_calculator(Optimizer): """Function to set up a fixed region calculator for use with LAMMPS and ASE """ calc = self.calc pms = copy.deepcopy(calc.parameters) nat = sum([c for sym, c, m, mu in self.atomlist]) try: pms['mass'][len(pms['mass']) - 1] += '\ngroup RO id >= ' + repr( nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n' except KeyError: pms['pair_coeff'][0] += '\ngroup RO id >= ' + repr( nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n' ncalc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir) return ncalc
from MAST.structopt_stem.io.read_xyz import read_xyz from MAST.structopt_stem.io.write_xyz import write_xyz from ase import Atom,Atoms from MAST.structopt_stem.tools.lammps import LAMMPS import os # Set up calculator parcoff = '* * FeCr.cdeam Cr Fe' pair_coeff = [parcoff] parameters = { 'pair_style' : 'eam/cd', 'pair_coeff' : pair_coeff } mincomd = '1e-8 1e-8 5000 10000' parameters['minimize'] = mincomd filesL = [ 'FeCr.cdeam' ] calc = LAMMPS(parameters=parameters, files=filesL, keep_tmp_files=True, tmp_dir=os.path.join(os.getcwd(), 'LAMMPSFiles')) files = os.listdir(os.getcwd()) files = [file for file in files if '.xyz' in file] for file in flist: # Read File structure = read_xyz(file,-1) # Calculate Energy structure.set_cell([22.96, 22.96, 22.96]) structure.set_pbc(True) structure.set_calculator(calc) OUT=structure.calc.calculate(structure) totalsol=OUT['atoms'] totalsol.set_pbc(True) en=OUT['thermo'][-1]['pe'] #Write Relaxed Structure write_xyz('r{0}'.format(file),totalsol,repr(en)) fe = en
def setup_calculator(Optimizer): """ Subprogram to set up the ASE style calculator for a system Input: Optimizer = Optimizer class object with parameters for setting up calculator Output: calc = ASE Calculator object for running a calculation """ if 'SetCalc' in Optimizer.debug: debug = True #logger = initialize_logger(Optimizer.loggername) logger = logging.getLogger(Optimizer.loggername) else: debug = False atomlist = Optimizer.atomlist #atomlist=sorted(atomlist,key=lambda symbol: symbol[0]) if Optimizer.calc_method == 'VASP': if debug: logger.info('Setting up vasp calculator = {0}'.format( Optimizer.vaspcalc)) calc = eval(Optimizer.vaspcalc) elif 'MAST' in Optimizer.calc_method: if debug: logger.info('Setting up dummy calculator for MAST') calc = LennardJones() elif Optimizer.calc_method == 'LennardJones': if debug: logger.info('Setting up Lennard Jones calculator from ASE') calc = LennardJones() else: if Optimizer.pair_style == 'tersoff': if debug: logger.info( 'Setting up LAMMPS calculator with Tersoff potential') parcoff = '* * {0}'.format(Optimizer.pot_file) for one in atomlist: parcoff += ' {0}'.format(one[0]) pair_coeff = [parcoff] mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = { 'pair_style' : Optimizer.pair_style, \ 'pair_coeff' : pair_coeff , 'mass' : mass } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'eam': if debug: logger.info('Setting up LAMMPS calculator with EAM potential') pair_coeff = ['* * {0}'.format(Optimizer.pot_file)] parameters = { 'pair_style': Optimizer.pair_style, 'pair_coeff': pair_coeff } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'eam/fs' or Optimizer.pair_style == 'eam/alloy': if debug: logger.info( 'Setting up LAMMPS calculator with EAM/FS , EAM/ALLOY potential' ) parcoff = '* * {0}'.format(Optimizer.pot_file) for one in atomlist: parcoff += ' {0}'.format(one[0]) pair_coeff = [parcoff] mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = { 'pair_style': Optimizer.pair_style, 'pair_coeff': pair_coeff, 'mass': mass } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'eam/cd': if debug: logger.info( 'Setting up LAMMPS calculator with EAM/CD potential') parcoff = '* * {0}'.format(Optimizer.pot_file) for one in atomlist: parcoff += ' {0}'.format(one[0]) pair_coeff = [parcoff] parameters = { 'pair_style': Optimizer.pair_style, 'pair_coeff': pair_coeff } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'edip': if debug: logger.info('Setting up LAMMPS calculator with EDIP potential') parcoff = '* * {0}'.format(Optimizer.pot_file) for one in atomlist: parcoff += ' {0}'.format(one[0]) pair_coeff = [parcoff] mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = { 'pair_style' : Optimizer.pair_style, \ 'pair_coeff' : pair_coeff , 'mass' : mass, 'newton': 'on' } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'bop': if debug: logger.info('Setting up LAMMPS calculator with BOP potential') parcoff = '* * {0}'.format(Optimizer.pot_file) for one in atomlist: parcoff += ' {0}'.format(one[0]) parcoff += '\ncommunicate single cutoff {0}'.format( Optimizer.bopcutoff) pair_coeff = [parcoff] mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = { 'pair_style' : Optimizer.pair_style, \ 'pair_coeff' : pair_coeff, 'mass' : mass, 'newton': 'on' } filesL = [Optimizer.pot_file] elif Optimizer.pair_style == 'buck': if debug: logger.info( 'Setting up LAMMPS calculator with Buckingham potential') pairstyle = '{0} {1}'.format(Optimizer.pair_style, Optimizer.buckcutoff) pair_coeff = Optimizer.buckparameters mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = {'pair_style': pairstyle, 'pair_coeff': pair_coeff, \ 'mass' : mass } filesL = None ## ZS elif 'lj' in Optimizer.pair_style: if debug: logger.info( 'Setting up LAMMPS calculator with Lennard Jones potential' ) pairstyle = Optimizer.pair_style pair_coeff = [Optimizer.pair_coeff] mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) parameters = { 'pair_style' : Optimizer.pair_style, \ 'pair_coeff' : pair_coeff, 'mass' : mass} filesL = None elif Optimizer.pair_style == 'other': """WARNING: This style still needs work. Intended to allow user flexibility with potential specification""" if debug: logger.info( 'Setting up LAMMPS calculator with user input potential') mass = ['1 {0}'.format(atomlist[0][2])] if len(atomlist) > 1: for i in range(len(atomlist) - 1): mass.append('{0} {1}'.format(i + 2, atomlist[i + 1][2])) if Optimizer.ps_other != None: logger.info( 'Setting up LAMMPS calculator with EAM/FS , EAM/ALLOY potential' ) if 'newton' in Optimizer.ps_other: parameters = {'pair_style' : Optimizer.ps_name, \ 'pair_coeff': [Optimizer.pair_coeff], 'mass': mass,'newton':'on'} else: parameters = {'pair_style' : Optimizer.ps_name, \ 'pair_coeff': [Optimizer.pair_coeff], 'mass': mass,'newton':'off'} if 'charges' in Optimizer.ps_other: cs = Optimizer.ps_other.split('charges:') parameters['mass'][len(parameters['mass']) - 1] += cs[1] parameters['newton'] += '\natom_style charge' else: parameters = {'pair_style' : Optimizer.ps_name, \ 'pair_coeff': Optimizer.pair_coeff, 'mass': mass} if Optimizer.pot_file != None: filesL = Optimizer.pot_file else: filesL = None else: if debug: logger.warn( 'No LAMMPS potential recognized. Setting up LAMMPS calculator with Lennard Jones potential' ) parameters = {} filesL = None print 'WARNING: No LAMMPS potential recognized. Assuming Lennard Jones Potential' if Optimizer.lammps_min != None: if debug: logger.info( 'Adding local energy minimizer to LAMMPS calculator') try: parameters['mass'][len(parameters['mass']) - 1] += '\nmin_style {0}'.format( Optimizer.lammps_min_style) except KeyError: parameters['pair_coeff'][0] += '\nmin_style {0}'.format( Optimizer.lammps_min_style) parameters['minimize'] = Optimizer.lammps_min parameters['thermosteps'] = Optimizer.lammps_thermo_steps if Optimizer.lammps_command != None: parameters['lammps_command'] = Optimizer.lammps_command if Optimizer.lammps_keep_files: if debug: logger.info('Setting up directory for keeping LAMMPS files') try: rank = MPI.COMM_WORLD.Get_rank() if Optimizer.parallel: if 'Island_Method' not in Optimizer.algorithm_type: real_rank = MPI.COMM_WORLD.Get_rank() 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')) logger.info('Making directory: {0}'.format( os.path.join(path, 'LAMMPSFiles'))) except: rank = 0 if filesL != None: path = os.path.join( os.getcwd(), '{0}-rank{1}'.format(Optimizer.filename, rank)) if Optimizer.parallel and ('Island_Method' not in Optimizer.algorithm_type): tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'), 'rank-{0}'.format(real_rank)) calc = LAMMPS(parameters=parameters, files=filesL, \ keep_tmp_files=True, tmp_dir=tmpdir) else: calc = LAMMPS(parameters=parameters, files=filesL, \ keep_tmp_files=True, tmp_dir=os.path.join(path, 'LAMMPSFiles')) else: path = os.path.join( os.getcwd(), '{0}-rank{1}'.format(Optimizer.filename, rank)) # calc = LAMMPS(parameters=parameters, keep_tmp_files=True, \ # tmp_dir=os.path.join(path,'LAMMPSFiles')) if Optimizer.parallel and ('Island_Method' not in Optimizer.algorithm_type): tmpdir = os.path.join(os.path.join(path, 'LAMMPSFiles'), 'rank-{0}'.format(real_rank)) calc = LAMMPS(parameters=parameters, \ keep_tmp_files=True, tmp_dir=tmpdir) else: calc = LAMMPS(parameters=parameters, \ keep_tmp_files=True, tmp_dir=os.path.join(path, 'LAMMPSFiles')) else: if filesL != None: calc = LAMMPS(parameters=parameters, files=filesL) else: calc = LAMMPS(parameters=parameters) return calc
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 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': # logger.info('M:') 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() #print 'rank, eval_energy.cell',rank,origcell if Optimizer.forcing != 'RelaxBox': 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]) # logger.info('M: set cell') 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') # logger.info('M:check dist') totalsol, STR = check_min_dist(Optimizer, 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: # logger.info('M:start calculator') 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, pea, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, Optimizer.fixed_region, Optimizer.fitness_scheme, STR, Optimizer.static_calc) else: # logger.info('M:start run_energy_eval') totalsol, pea, energy, pressure, volume, STR = run_energy_eval(totalsol, Optimizer.calc_method, False, Optimizer.fitness_scheme, STR) logger.info('M:finish run_energy_eval, energy = {0} @ rank ={1}'.format(energy,rank)) 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') if Optimizer.forcing != 'RelaxBox': 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 #Add pealist to include atom index based on sorted PE. logger.info('before sort{0}'.format(individ.energy)) sort_pealist(Optimizer,individ,pea) energy = individ.energy logger.info('after sort {0}'.format(individ.energy)) 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 eval_energy(input): """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 """ if input[0] == None: energy = 0 bul = 0 individ = 0 rank = MPI.COMM_WORLD.Get_rank() signal = 'Evaluated none individual on ' + repr(rank) + '\n' else: [Optimizer, individ] = input if Optimizer.calc_method == 'MAST': energy = individ.energy bul = individ.energy signal = 'Recieved MAST structure\n' else: if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank() if not Optimizer.genealogy: STR = '----Individual ' + str( individ.index) + ' Optimization----\n' else: 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, 'Recieved by eval_energy') Optimizer.debugfile.flush() if Optimizer.structure == 'Defect': indi = indiv.copy() if Optimizer.alloy == True: bulk = individ.bulki else: bulk = individ.bulko nat = indi.get_number_of_atoms() 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) 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]) if Optimizer.constrain_position: ts = totalsol.copy() indc, indb, vacant, swap, stro = find_defects( ts, Optimizer.solidbulk, 0) sbulk = Optimizer.solidbulk.copy() bcom = sbulk.get_center_of_mass() #totalsol.translate(-bulkcom) #indc.translate(-bulkcom) #totalsol.append(Atom(position=[0,0,0])) # for one in indc: # index = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0] # if totalsol.get_distance(-1,index) > Optimizer.sf: # r = random.random() # totalsol.set_distance(-1,index,Optimizer.sf*r,fix=0) # totalsol.pop() # totalsol.translate(bulkcom) com = indc.get_center_of_mass() dist = (sum((bcom[i] - com[i])**2 for i in range(3)))**0.5 if dist > Optimizer.sf: STR += 'Shifting structure to within region\n' r = random.random() * Optimizer.sf comv = numpy.linalg.norm(com) ncom = [one * r / comv for one in com] trans = [ncom[i] - com[i] for i in range(3)] indices = [] for one in indc: id = [ atm.index for atm in totalsol if atm.position[0] == one.position[0] and atm.position[1] == one.position[1] and atm.position[2] == one.position[2] ][0] totalsol[id].position += trans # Check for atoms that are too close min_len = 0.7 #pdb.set_trace() if not Optimizer.fixed_region: if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface': cutoffs = [2.0 for one in totalsol] nl = NeighborList(cutoffs, bothways=True, self_interaction=False) nl.update(totalsol) for one in totalsol[0:nat]: nbatoms = Atoms() nbatoms.append(one) indices, offsets = nl.get_neighbors(one.index) for index, d in zip(indices, offsets): index = int(index) sym = totalsol[index].symbol pos = totalsol[index].position + numpy.dot( d, totalsol.get_cell()) at = Atom(symbol=sym, position=pos) nbatoms.append(at) while True: dflag = False for i in range(1, len(nbatoms)): d = nbatoms.get_distance(0, i) if d < min_len: nbatoms.set_distance(0, i, min_len + .01, fix=0.5) STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n' dflag = True if dflag == False: break for i in range(len(indices)): totalsol[indices[i]].position = nbatoms[i + 1].position totalsol[one.index].position = nbatoms[0].position nl.update(totalsol) if debug: write_xyz(Optimizer.debugfile, totalsol, 'After minlength check') Optimizer.debugfile.flush() else: for i in range(len(indiv)): for j in range(len(indiv)): if i != j: d = indiv.get_distance(i, j) if d < min_len: indiv.set_distance(i, j, min_len, fix=0.5) STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n' if debug: write_xyz(Optimizer.debugfile, indiv, 'After minlength check') Optimizer.debugfile.flush() # Set calculator to use to get forces/energies if Optimizer.parallel: calc = setup_calculator(Optimizer) if Optimizer.fixed_region: pms = copy.deepcopy(calc.parameters) try: pms['mass'][ len(pms['mass']) - 1] += '\ngroup RO id >= ' + repr( nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n' except KeyError: pms['pair_coeff'][0] += '\ngroup RO id >= ' + repr( nat) + '\nfix freeze RO setforce 0.0 0.0 0.0\n' 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) Optimizer.lammps_min = None Optimizer.static_calc = setup_calculator(Optimizer) Optimizer.lammps_min = lmin else: calc = Optimizer.calc if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface': totalsol.set_calculator(calc) totalsol.set_pbc(True) else: indiv.set_calculator(calc) indiv.set_pbc( True) #Current bug in ASE optimizer-Lammps prevents pbc=false if Optimizer.structure == 'Cluster': indiv.set_cell([500, 500, 500]) indiv.translate([250, 250, 250]) cwd = os.getcwd() # Perform Energy Minimization if not Optimizer.parallel: Optimizer.output.flush() if Optimizer.ase_min == True: try: if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface': dyn = BFGS(totalsol) else: dyn = BFGS(indiv) dyn.run(fmax=Optimizer.ase_min_fmax, steps=Optimizer.ase_min_maxsteps) except OverflowError: STR += '--- Error: Infinite Energy Calculated - Implement Random ---\n' box = Atoms() indiv = gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size) indiv.set_calculator(calc) dyn = BFGS(indiv) dyn.run(fmax=fmax, steps=steps) except numpy.linalg.linalg.LinAlgError: STR += '--- Error: Singular Matrix - Implement Random ---\n' indiv = gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size) indiv.set_calculator(calc) dyn = BFGS(indiv) dyn.run(fmax=fmax, steps=steps) # Get Energy of Minimized Structure if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface': en = totalsol.get_potential_energy() #force=numpy.maximum.reduce(abs(totalsol.get_forces())) if Optimizer.fitness_scheme == 'enthalpyfit': pressure = totalsol.get_isotropic_pressure( totalsol.get_stress()) cell_max = numpy.maximum.reduce(totalsol.get_positions()) cell_min = numpy.minimum.reduce(totalsol.get_positions()) cell = cell_max - cell_min volume = cell[0] * cell[1] * cell[2] else: pressure = 0 volume = 0 na = totalsol.get_number_of_atoms() ena = en / na energy = en individ[0] = totalsol[0:nat] bul = totalsol[(nat):len(totalsol)] STR += 'Number of positions = ' + repr( len(bul) + len(individ[0])) + '\n' individ[0].set_cell(csize) indiv = individ[0] else: en = indiv.get_potential_energy() if Optimizer.fitness_scheme == 'enthalpyfit': pressure = indiv.get_isotropic_pressure(indiv.get_stress()) cell_max = numpy.maximum.reduce(indiv.get_positions()) cell_min = numpy.minimum.reduce(indiv.get_positions()) cell = cell_max - cell_min volume = cell[0] * cell[1] * cell[2] else: pressure = 0 volume = 0 na = indiv.get_number_of_atoms() ena = en / na energy = ena individ[0] = indiv bul = 0 else: if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface': if Optimizer.calc_method == 'VASP': en = totalsol.get_potential_energy() calcb = Vasp(restart=True) totalsol = calcb.get_atoms() stress = calcb.read_stress() else: try: totcop = totalsol.copy() if debug: write_xyz(Optimizer.debugfile, totcop, 'Individual sent to lammps') OUT = totalsol.calc.calculate(totalsol) totalsol = OUT['atoms'] totalsol.set_pbc(True) if Optimizer.fixed_region: if debug: print 'Energy of fixed region calc = ', OUT[ 'thermo'][-1]['pe'] totalsol.set_calculator(Optimizer.static_calc) OUT = totalsol.calc.calculate(totalsol) totalsol = OUT['atoms'] totalsol.set_pbc(True) if debug: print 'Energy of static calc = ', OUT[ 'thermo'][-1]['pe'] en = OUT['thermo'][-1]['pe'] stress = numpy.array([ OUT['thermo'][-1][i] for i in ('pxx', 'pyy', 'pzz', 'pyz', 'pxz', 'pxy') ]) * (-1e-4 * GPa) #force=numpy.maximum.reduce(abs(totalsol.get_forces())) if debug: write_xyz(Optimizer.debugfile, totalsol, 'After Lammps Minimization') Optimizer.debugfile.flush() except Exception, e: os.chdir(cwd) STR += 'WARNING: Exception during energy eval:\n' + repr( e) + '\n' f = open('problem-structures.xyz', 'a') write_xyz(f, totcop, data='Starting structure hindex=' + individ.history_index) write_xyz(f, totalsol, data='Lammps Min structure') en = 10 stress = 0 f.close() if Optimizer.fitness_scheme == 'enthalpyfit': pressure = totalsol.get_isotropic_pressure(stress) cell_max = numpy.maximum.reduce(totalsol.get_positions()) cell_min = numpy.minimum.reduce(totalsol.get_positions()) cell = cell_max - cell_min volume = cell[0] * cell[1] * cell[2] else: pressure = totalsol.get_isotropic_pressure(stress) volume = 0 na = totalsol.get_number_of_atoms() ena = en / na energy = en if Optimizer.structure == 'Defect': if Optimizer.fixed_region == True or Optimizer.finddefects == False: individ[0] = totalsol[0:nat] bul = totalsol[(nat):len(totalsol)] individ[0].set_cell(csize) else: if 'FI' 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] else: top, bul = find_top_layer(totalsol, Optimizer.surftopthick) indiv = top.copy() individ[0] = top.copy() else:
from MAST.structopt_stem.tools.lammps import LAMMPS # Set up calculator parcoff = '* * SiC.edip C Si' pair_coeff = [parcoff] mass = ['1 12.011', '2 28.0855'] parameters = { 'pair_style': 'edip', 'pair_coeff': pair_coeff, 'mass': mass, 'newton': 'on' } mincomd = '1e-8 1e-8 5000 10000' parameters['minimize'] = mincomd filesL = ['SiC.edip'] calc = LAMMPS(parameters=parameters, files=filesL) # Read File structure = read_xyz('indiv00.xyz', -1) # Calculate Energy structure.set_cell([13.092, 13.092, 13.092]) structure.set_pbc(True) structure.set_calculator(calc) OUT = structure.calc.calculate(structure) totalsol = OUT['atoms'] totalsol.set_pbc(True) en = OUT['thermo'][-1]['pe'] #Write Relaxed Structure write_xyz('re-relaxed.xyz', totalsol, repr(en)) fe = en