def run(i=0, edir=''):
from sys import path
path.append(edir)
from kmos.run import KMC_Model
model = KMC_Model(banner=False, print_rates=False)
model.settings.random_seed = i
assert not model.do_steps(1000)
assert not model.deallocate()
def run(i=0, edir=''):
from sys import path
path.append(edir)
from kmos.run import KMC_Model
model = KMC_Model(banner=False, print_rates=False)
model.settings.random_seed = i
assert not model.do_steps(1000)
assert not model.deallocate()
def main(args=None):
"""The CLI main entry point function.
The optional argument args, can be used to
directly supply command line argument like
$ kmos <args>
otherwise args will be taken from STDIN.
"""
from glob import glob
options, args, parser = get_options(args, get_parser=True)
global model, pt, np, cm_model
if not args[0] in usage.keys():
args[0] = match_keys(args[0], usage, parser)
if args[0] == 'benchmark':
from sys import path
path.append(os.path.abspath(os.curdir))
nsteps = 1000000
from time import time
from kmos.run import KMC_Model
model = KMC_Model(print_rates=False, banner=False)
time0 = time()
try:
model.proclist.do_kmc_steps(nsteps)
except: # kmos < 0.3 had no model.proclist.do_kmc_steps
model.do_steps(nsteps)
needed_time = time() - time0
print('Using the [%s] backend.' % model.get_backend())
print('%s steps took %.2f seconds' % (nsteps, needed_time))
print('Or %.2e steps/s' % (1e6 / needed_time))
model.deallocate()
elif args[0] == 'build':
from kmos.utils import build
build(options)
elif args[0] == 'edit':
from kmos import gui
gui.main()
elif args[0] == 'settings-export':
import kmos.types
import kmos.io
from kmos.io import ProcListWriter
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = '%s_%s' % (os.path.splitext(args[1])[0], options.backend)
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = args[2]
project = kmos.types.Project()
project.import_file(xml_file)
writer = ProcListWriter(project, export_dir)
writer.write_settings()
elif args[0] == 'export':
import kmos.types
import kmos.io
from kmos.utils import build
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = '%s_%s' % (os.path.splitext(args[1])[0], options.backend)
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = os.path.join(args[2], 'src')
project = kmos.types.Project()
project.import_file(xml_file)
project.shorten_names(max_length=options.variable_length)
kmos.io.export_source(project, export_dir, options=options)
if ((os.name == 'posix'
and os.uname()[0] in ['Linux', 'Darwin'])
or os.name == 'nt') \
and not options.source_only:
os.chdir(export_dir)
build(options)
for out in glob('kmc_*'):
if os.path.exists('../%s' % out):
if options.overwrite:
overwrite = 'y'
else:
overwrite = raw_input(
('Should I overwrite existing %s ?'
'[y/N] ') % out).lower()
if overwrite.startswith('y'):
print('Overwriting {out}'.format(**locals()))
os.remove('../%s' % out)
shutil.move(out, '..')
else:
print('Skipping {out}'.format(**locals()))
else:
shutil.move(out, '..')
elif args[0] == 'settings-export':
import kmos.io
pt = kmos.io.import_file(args[1])
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting kmc_settings.py to %s' %
out_dir)
args.append(out_dir)
if not os.path.exists(args[2]):
os.mkdir(args[2])
elif not os.path.isdir(args[2]):
raise UserWarning("Cannot overwrite %s; Exiting;" % args[2])
writer = kmos.io.ProcListWriter(pt, args[2])
writer.write_settings()
elif args[0] == 'help':
if len(args) < 2:
parser.error('Which help do you want?')
if args[1] == 'all':
for command in sorted(usage):
print(usage[command])
elif args[1] in usage:
print('Usage: %s\n' % usage[args[1]])
else:
arg = match_keys(args[1], usage, parser)
print('Usage: %s\n' % usage[arg])
elif args[0] == 'import':
import kmos.io
if not len(args) >= 2:
raise UserWarning('XML file name expected.')
pt = kmos.io.import_xml_file(args[1])
if len(args) == 2:
sh(banner='Note: pt = kmos.io.import_xml(\'%s\')' % args[1])
elif len(
args
) == 3: # if optional 3rd argument is given, store model there and exit
pt.save(args[2])
elif args[0] == 'rebuild':
from time import sleep
print('Will rebuild model from kmc_settings.py in current directory')
print('Please do not interrupt,'
' build process, as you will most likely')
print('loose the current model files.')
sleep(2.)
from sys import path
path.append(os.path.abspath(os.curdir))
from tempfile import mktemp
if not os.path.exists('kmc_model.so') \
and not os.path.exists('kmc_model.pyd'):
raise Exception('No kmc_model.so found.')
if not os.path.exists('kmc_settings.py'):
raise Exception('No kmc_settings.py found.')
from kmos.run import KMC_Model
model = KMC_Model(print_rates=False, banner=False)
tempfile = mktemp()
f = file(tempfile, 'w')
f.write(model.xml())
f.close()
for kmc_model in glob('kmc_model.*'):
os.remove(kmc_model)
os.remove('kmc_settings.py')
main('export %s -b %s .' % (tempfile, options.backend))
os.remove(tempfile)
model.deallocate()
elif args[0] in ['run', 'shell']:
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
# useful to have in interactive mode
import numpy as np
try:
from matplotlib import pyplot as plt
except:
plt = None
if options.catmap:
import catmap
import catmap.cli.kmc_runner
seed = catmap.cli.kmc_runner.get_seed_from_path('.')
cm_model = catmap.ReactionModel(setup_file='{seed}.mkm'.format(
**locals()))
catmap_message = '\nSide-loaded catmap_model {seed}.mkm into cm_model = ReactionModel(setup_file="{seed}.mkm")'.format(
**locals())
else:
catmap_message = ''
try:
model = KMC_Model(print_rates=False)
except:
print("Warning: could not import kmc_model!"
" Please make sure you are in the right directory")
sh(banner='Note: model = KMC_Model(print_rates=False){catmap_message}'.
format(**locals()))
try:
model.deallocate()
except:
print("Warning: could not deallocate model. Was is allocated?")
elif args[0] == 'version':
from kmos import VERSION
print(VERSION)
elif args[0] == 'view':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos import view
view.main(steps_per_frame=options.steps_per_frame)
elif args[0] == 'xml':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
model = KMC_Model(banner=False, print_rates=False)
print(model.xml())
else:
parser.error('Command "%s" not understood.' % args[0])
import math
from kmos.run import KMC_Model
model = KMC_Model(banner=False)
model.parameters.p_COgas = 2.e-1
model.parameters.p_O2gas = 1.e-1
nrel = 1e7
nsample = 1e7 # numerical parameters
Ts = range(450, 650, 20) # 20 values between 450 and 650 K
TOFs = [] # empty list for output
# Loop over the temperature
for T in Ts:
model.parameters.T = T # Set the temperature
model.do_steps(nrel) # Relax the system
# Sample the reactivity
output = model.get_std_sampled_data(1, nsample, output='dict')
# Collect output
TOFs.append(output['CO_oxidation'])
# Transform the variables
invTs = [1 / float(T) for T in Ts]
logTOFs = [math.log(TOF, 10.) for TOF in TOFs]
# and plot
import matplotlib.pyplot as plt
plt.plot(invTs, logTOFs, '-o')
plt.xlabel('1/T [1/K]')
plt.ylabel('log(TOF) / events (sites s)^-1')
plt.savefig('arrhenius.pdf') # Optionally, save plot
def main(args=None):
"""The CLI main entry point function.
The optional argument args, can be used to
directly supply command line argument like
$ kmos <args>
otherwise args will be taken from STDIN.
"""
from glob import glob
options, args, parser = get_options(args, get_parser=True)
if not args[0] in usage.keys():
args[0] = match_keys(args[0], usage, parser)
if args[0] == 'benchmark':
from sys import path
path.append(os.path.abspath(os.curdir))
nsteps = 1000000
from time import time
from kmos.run import KMC_Model
model = KMC_Model(print_rates=False, banner=False)
time0 = time()
try:
model.proclist.do_kmc_steps(nsteps)
except: # kmos < 0.3 had no model.proclist.do_kmc_steps
model.do_steps(nsteps)
needed_time = time() - time0
print('Using the [%s] backend.' % model.get_backend())
print('%s steps took %.2f seconds' % (nsteps, needed_time))
print('Or %.2e steps/s' % (1e6 / needed_time))
model.deallocate()
elif args[0] == 'build':
from kmos.utils import build
build(options)
elif args[0] == 'edit':
from kmos import gui
gui.main()
elif args[0] == 'settings-export':
import kmos.types
import kmos.io
from kmos.io import ProcListWriter
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = args[2]
project = kmos.types.Project()
project.import_xml_file(xml_file)
writer = ProcListWriter(project, export_dir)
writer.write_settings()
elif args[0] == 'export':
import kmos.types
import kmos.io
from kmos.utils import build
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = '%s_%s' % (os.path.splitext(args[1])[0], options.backend)
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = os.path.join(args[2], 'src')
project = kmos.types.Project()
project.import_xml_file(xml_file)
kmos.io.export_source(project,
export_dir,
code_generator=options.backend)
if ((os.name == 'posix'
and os.uname()[0] == 'Linux')
or os.name == 'nt') \
and not options.source_only:
os.chdir(export_dir)
build(options)
for out in glob('kmc_*'):
if os.path.exists('../%s' % out):
overwrite = raw_input(('Should I overwrite existing %s ?'
'[y/N] ') % out).lower()
if overwrite.startswith('y'):
os.remove('../%s' % out)
shutil.move(out, '..')
else:
shutil.move(out, '..')
elif args[0] == 'settings-export':
import kmos.io
pt = kmos.io.import_xml_file(args[1])
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting kmc_settings.py to %s'
% out_dir)
args.append(out_dir)
if not os.path.exists(args[2]):
os.mkdir(args[2])
elif not os.path.isdir(args[2]):
raise UserWarning("Cannot overwrite %s; Exiting;" % args[2])
writer = kmos.io.ProcListWriter(pt, args[2])
writer.write_settings()
elif args[0] == 'help':
if len(args) < 2:
parser.error('Which help do you want?')
if args[1] == 'all':
for command in sorted(usage):
print(usage[command])
elif args[1] in usage:
print('Usage: %s\n' % usage[args[1]])
else:
arg = match_keys(args[1], usage, parser)
print('Usage: %s\n' % usage[arg])
elif args[0] == 'import':
import kmos.io
if not len(args) >= 2:
raise UserWarning('XML file name expected.')
global pt
pt = kmos.io.import_xml_file(args[1])
sh(banner='Note: pt = kmos.io.import_xml(\'%s\')' % args[1])
elif args[0] == 'rebuild':
from time import sleep
print('Will rebuild model from kmc_settings.py in current directory')
print('Please do not interrupt,'
' build process, as you will most likely')
print('loose the current model files.')
sleep(2.)
from sys import path
path.append(os.path.abspath(os.curdir))
from tempfile import mktemp
if not os.path.exists('kmc_model.so') \
and not os.path.exists('kmc_model.pyd'):
raise Exception('No kmc_model.so found.')
if not os.path.exists('kmc_settings.py'):
raise Exception('No kmc_settings.py found.')
from kmos.run import KMC_Model
model = KMC_Model(print_rates=False, banner=False)
tempfile = mktemp()
f = file(tempfile, 'w')
f.write(model.xml())
f.close()
for kmc_model in glob('kmc_model.*'):
os.remove(kmc_model)
os.remove('kmc_settings.py')
main('export %s -b %s .' % (tempfile, options.backend))
os.remove(tempfile)
model.deallocate()
elif args[0] in ['run', 'shell']:
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
# useful to have in interactive mode
import numpy as np
try:
from matplotlib import pyplot as plt
except:
plt = None
try:
model = KMC_Model(print_rates=False)
except:
print("Warning: could not import kmc_model!"
" Please make sure you are in the right directory")
global model, np
sh(banner='Note: model = KMC_Model(print_rates=False)')
try:
model.deallocate()
except:
print("Warning: could not deallocate model. Was is allocated?")
elif args[0] == 'version':
from kmos import VERSION
print(VERSION)
elif args[0] == 'view':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos import view
view.main(steps_per_frame=options.steps_per_frame)
elif args[0] == 'xml':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
model = KMC_Model(banner=False, print_rates=False)
print(model.xml())
else:
parser.error('Command "%s" not understood.' % args[0])
#prepare arrays for TOFs, coverages and kmc steps
tofs = np.zeros((N, len(tof_labels)))
covs = np.zeros((N, len(cov_labels)))
steps = np.zeros((N, 1))
#run model and save data
for i in range(N):
atoms = model.get_atoms(geometry=False)
tof = atoms.tof_integ
tofs[i, :] = tof
cov = atoms.occupation
covs[i, :] = cov.flatten()
step = atoms.kmc_step
steps[i] = step
model.do_steps(sample_step)
#prepare figure and plot colors
fig = pylab.figure()
colors = [
"#0065bd", "#a2ad00", "#e37222", "#B452CD", "#dad7cb", "#000000", "r"
]
#plot TOFs
ax = fig.add_subplot(2, 1, 1)
for i in range(len(tof_labels)):
ax.plot(steps, tofs[:, i], color=colors[i], label='CO2')
ax.set_xlabel('kmc steps')
ax.set_ylabel(ur'TOF (s$^{-1}$site$^{-1}$)')
#pylab.ylim([0,5])
box = ax.get_position()
n_relax = 1e7
n_sample = 1e7
eps_f = 0.02
e_int = 0.002
thetas = np.linspace(0.1, 0.9, 9)
# current vs. concentration
currents = []
for theta in thetas:
model = KMC_Model(banner=False)
model.parameters.thetaS = theta
model.parameters.thetaD = theta
model.parameters.eps_f = eps_f
model.parameters.e_int = e_int
model.do_steps(n_relax)
exit0 = (model.base.get_procstat(model.proclist.drain_exit) -
model.base.get_procstat(model.proclist.drain_entry))
t0 = model.base.get_kmc_time()
model.do_steps(n_sample)
currents.append(
(model.base.get_procstat(model.proclist.drain_exit) -
model.base.get_procstat(model.proclist.drain_entry) - exit0) /
(model.base.get_kmc_time() - t0) / float(model.size[1]))
model.deallocate()
fig, ax = plt.subplots(1)
ax.plot(thetas, currents, '-o')
ax.set_xlabel('Concentration')
"""
import math
from kmos.run import KMC_Model
model = KMC_Model(banner = False)
model.parameters.p_COgas = 2.e-1
model.parameters.p_O2gas = 1.e-1
nrel = 1e7; nsample = 1e7 # numerical parameters
Ts = range(450,650,20) # 20 values between 450 and 650 K
TOFs = [] # empty list for output
# Loop over the temperature
for T in Ts:
model.parameters.T = T # Set the temperature
model.do_steps(nrel) # Relax the system
# Sample the reactivity
output = model.get_std_sampled_data(1, nsample, output='dict')
# Collect output
TOFs.append(output['CO_oxidation'])
# Transform the variables
invTs = [1/float(T) for T in Ts]
logTOFs = [math.log(TOF,10.) for TOF in TOFs]
# and plot
import matplotlib.pyplot as plt
plt.plot(invTs, logTOFs, '-o')
plt.xlabel('1/T [1/K]')
plt.ylabel('log(TOF) / events (sites s)^-1')
plt.savefig('arrhenius.pdf') # Optionally, save plot
from kmos.run import KMC_Model
import random
Ts = [350, 450]
kads = 3e-3
size = (30, 30, 30)
targetML = 4.
nsteps = 100
for i, T in enumerate(Ts):
random_seed = random.random() * 1e12
model = KMC_Model(banner=False, size=size, random_seed=random_seed)
model.parameters.T = T
model.parameters.kads = kads
tsim = 0.0
ML = 0.0
while ML < targetML:
model.do_steps(nsteps)
at = model.get_atoms(geometry=False)
# Convert TOF into ML growth
ML += at.tof_data[model.tofs.index('Growth')] * at.delta_t * size[2]
outname = '_'.join(['config', 'T{}'.format(T)] +
['{}'.format(d) for d in model.size])
model.dump_config(outname)
print('Finished with T={}K'.format(T))
print('Deposited {}ML in {} s'.format(ML, model.base.get_kmc_time()))
model.deallocate()
#view(atoms)
#get DRC for CO adsorption on cus site
process = "CO_adsorption_cus"
#in finite-difference derivative, change rate constant by plus/minus 2%
delta = 0.02
#relax_steps
relax_steps = 1e6
#sample_steps
sample_steps = 1e7
#relax model
model.do_steps(relax_steps)
atoms = model.get_atoms(geometry=False)
#get rate constant
k = float(model.rate_constants(process).split('=')[1][1:-8])
#get initial TOF
k_ini = k * (1 - delta)
model.rate_constants.set("CO_adsorption_cus", k_ini)
data = model.get_std_sampled_data(samples=1,
sample_size=sample_steps,
tof_method="integ")
tof_ini = float(data.split(' ')[3])
#get final TOF
k_fin = k * (1 + delta)
n_relax = 1e7
n_sample = 1e7
eps_f = 0.02
e_int = 0.002
thetas = np.linspace(0.1, 0.9, 9)
# current vs. concentration
currents = []
for theta in thetas:
model = KMC_Model(banner=False)
model.parameters.thetaS = theta
model.parameters.thetaD = theta
model.parameters.eps_f = eps_f
model.parameters.e_int = e_int
model.do_steps(n_relax)
exit0 = (model.base.get_procstat(model.proclist.drain_exit)
- model.base.get_procstat(model.proclist.drain_entry))
t0 = model.base.get_kmc_time()
model.do_steps(n_sample)
currents.append((model.base.get_procstat(model.proclist.drain_exit)
- model.base.get_procstat(model.proclist.drain_entry)
- exit0) / (model.base.get_kmc_time() - t0) / float(model.size[1]))
model.deallocate()
fig, ax = plt.subplots(1)
ax.plot(thetas, currents, '-o')
ax.set_xlabel('Concentration')
ax.set_ylabel('Current')
Ts = [350, 450]
kads = 3e-3
size = (30, 30, 30)
targetML = 4.
nsteps = 100
for i,T in enumerate(Ts):
random_seed = random.random()*1e12
model = KMC_Model(banner=False,
size = size,
random_seed = random_seed)
model.parameters.T = T
model.parameters.kads = kads
tsim = 0.0
ML = 0.0
while ML < targetML:
model.do_steps(nsteps)
at = model.get_atoms(geometry=False)
# Convert TOF into ML growth
ML += at.tof_data[model.tofs.index('Growth')]*at.delta_t*size[2]
outname = '_'.join(['config', 'T{}'.format(T)] +
['{}'.format(d) for d in model.size])
model.dump_config(outname)
print('Finished with T={}K'.format(T))
print('Deposited {}ML in {} s'.format(
ML,
model.base.get_kmc_time()))
model.deallocate()
#view(atoms)
#get DRC for CO adsorption on cus site
process = "CO_adsorption_cus"
#in finite-difference derivative, change rate constant by plus/minus 2%
delta = 0.02
#relax_steps
relax_steps = 1e6
#sample_steps
sample_steps = 1e7
#relax model
model.do_steps(relax_steps)
atoms = model.get_atoms(geometry=False)
#get rate constant
k = float(model.rate_constants(process).split('=')[1][1:-8])
#get initial TOF
k_ini = k*(1-delta)
model.rate_constants.set("CO_adsorption_cus", k_ini)
data = model.get_std_sampled_data(samples=1,sample_size=sample_steps,tof_method="integ")
tof_ini = float(data.split(' ')[3])
#get final TOF
k_fin = k*(1+delta)
model.rate_constants.set("CO_adsorption_cus", k_fin)
data = model.get_std_sampled_data(samples=1,sample_size=sample_steps,tof_method="integ")
#prepare arrays for TOFs, coverages and kmc steps
tofs = np.zeros((N,len(tof_labels)))
covs = np.zeros((N,len(cov_labels)))
steps = np.zeros((N,1))
#run model and save data
for i in range(N):
atoms = model.get_atoms(geometry=False)
tof = atoms.tof_integ
tofs[i,:] = tof
cov = atoms.occupation
covs[i,:] = cov.flatten()
step = atoms.kmc_step
steps[i] = step
model.do_steps(sample_step)
#prepare figure and plot colors
fig = pylab.figure()
colors = ["#0065bd","#a2ad00","#e37222","#B452CD","#dad7cb","#000000","r"]
#plot TOFs
ax = fig.add_subplot(2,1,1)
for i in range(len(tof_labels)):
ax.plot(steps, tofs[:,i], color=colors[i], label='CO2')
ax.set_xlabel('kmc steps')
ax.set_ylabel(ur'TOF (s$^{-1}$site$^{-1}$)')
#pylab.ylim([0,5])
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.8, box.height])
ax.legend(bbox_to_anchor=(1, 0.916), bbox_transform=pylab.gcf().transFigure)
NREL = 1e7
NSAMPLE = 5e7
# current vs field
theta = 0.5
currents = []
fields = np.linspace(0.005, 0.04, 10)
for eps_f in fields:
model = KMC_Model(banner = False, size = [L, H])
model.parameters.thetaS = theta
model.parameters.thetaD = theta
model.parameters.eps_f = eps_f
model.do_steps(NREL)
exit0 = (model.base.get_procstat(model.proclist.drain_exit)
- model.base.get_procstat(model.proclist.drain_entry))
t0 = model.base.get_kmc_time()
model.do_steps(NSAMPLE)
currents.append( ( model.base.get_procstat(model.proclist.drain_exit)
- model.base.get_procstat(model.proclist.drain_entry)
- exit0) / (model.base.get_kmc_time() - t0) / float(L))
model.deallocate()
fig = plt.figure(figsize = (8, 5))
plt.plot(fields, currents, '-o')
plt.xlabel('Field contribution [eV]')
plt.ylabel('Current [ ions / (s site) ]')
plt.savefig('current_vs_field.pdf')
