def run_geo_opt(polymer, poly_size, smiles_list):
'''
Runs geometry optimization calculation on given polymer
Parameters
---------
polymer: list (specific format)
[(#,#,#,#), A, B]
poly_size: int
number of monomers per polymer
smiles_list: list
list of all possible monomer SMILES
'''
# make file name string w/ convention monoIdx1_monoIdx2_fullNumerSequence
file_name = utils.make_file_name(polymer, poly_size)
# if output file already exists, skip xTB
exists = os.path.isfile('output/%s.out' % (file_name))
if exists:
print("output file existed")
return
# make polymer into SMILES string
poly_smiles = utils.make_polymer_str(polymer, smiles_list, poly_size)
# make polymer string into pybel molecule object
mol = pybel.readstring('smi', poly_smiles)
utils.make3D(mol)
# write polymer .xyz file to containing folder
mol.write('xyz', 'input/%s.xyz' % (file_name), overwrite=True)
# make directory to run xtb in for the polymer
mkdir_poly = subprocess.call('(mkdir %s)' % (file_name), shell=True)
# run xTB geometry optimization
xtb = subprocess.call(
'(cd %s && /ihome/ghutchison/geoffh/xtb/xtb ../input/%s.xyz --opt >../output/%s.out)'
% (file_name, file_name, file_name),
shell=True)
save_opt_file = subprocess.call('(cp %s/xtbopt.xyz opt/%s_opt.xyz)' %
(file_name, file_name),
shell=True)
# delete xtb run directory for the polymer
del_polydir = subprocess.call('(rm -r %s)' % (file_name), shell=True)
params_SA['N_time_step'] = 100
params_SA['symmetrize'] = False
percentile = 99
fid_SA_group = {}
T_count = 0
for T in np.arange(0.1, 4.01, 0.1):
nQ_list = [
0, 100, 200, 300, 400, 500, 1000, 2000, 3000, 5000, 10000, 50000,
100000
]
for nQ in nQ_list:
params_SA['N_quench'] = nQ
params_SA['delta_t'] = T / 100
file_name = 'data/' + utils.make_file_name(params_SA)
tmp = []
with open(file_name, 'rb') as f:
#print(file_name)
data = pickle.load(f)
series = data[1]
for d in series:
tmp.append(d[1])
fidelity = np.mean(tmp)
#fidelity=np.percentile(tmp,percentile)
#fidelity=np.max(tmp)
fidelity_std = np.std(tmp)
fid_SA_group[(T_count, nQ)] = [fidelity, fidelity_std]
T_count += 1
#######################################
def next_gen(params):
'''
Runs one post-initial generation
Parameters
---------
params: list (specific format)
[pop_size, poly_size, num_mono_species, opt_property, smiles_list, sequence_list, mono_list, population, poly_property_list, n, gen_counter, spear_counter, prop_value_counter]
Returns
-------
params: list (specific format)
[pop_size, poly_size, num_mono_species, opt_property, smiles_list, sequence_list, mono_list, population, poly_property_list, n, gen_counter, spear_counter, prop_value_counter]
'''
# unpack parameters
pop_size = params[0]
poly_size = params[1]
num_mono_species = params[2]
opt_property = params[3]
smiles_list = params[4]
sequence_list = params[5]
mono_list = params[6]
population = params[7]
poly_property_list = params[8]
n = params[9]
gen_counter = params[10]
spear_counter = params[11]
prop_value_counter = params[12]
# open output files
analysis_file = open('gens_analysis.txt', 'a+')
population_file = open('gens_population.txt', 'a+')
values_file = open('gens_values.txt', 'a+')
if opt_property == 'dip':
dip_polar_file = open('gens_dip_polar.txt', 'a+')
if opt_property == 'pol':
polar_dip_file = open('gens_polar_dip.txt', 'a+')
spear_file = open('gens_spear.txt', 'a+')
gen_counter += 1
max_init = max(poly_property_list)
# create sorted monomer list with most freq first
gen1 = utils.sort_mono_indicies_list(mono_list)
# Selection - select heaviest (best) 50% of polymers as parents
population = parent_select(opt_property, population, poly_property_list)
# Crossover & Mutation - create children to repopulate bottom 50% of polymers in population
population = crossover_mutate(population, pop_size, poly_size,
num_mono_species, sequence_list, smiles_list,
mono_list)
# calculate desired polymer property
if opt_property == "mw":
poly_property_list = find_poly_mw(population, poly_size, smiles_list)
elif opt_property == "dip":
elec_prop_list = find_elec_prop(population, poly_size, smiles_list)
poly_property_list = elec_prop_list[0]
polar_list = elec_prop_list[1]
elif opt_property == 'pol':
elec_prop_list = find_elec_prop(population, poly_size, smiles_list)
poly_property_list = elec_prop_list[1]
dip_list = elec_prop_list[0]
else:
print(
"Error: opt_property not recognized. trace:main:loop pop properties"
)
# record representative generation properties
min_test = min(poly_property_list)
max_test = max(poly_property_list)
avg_test = mean(poly_property_list)
if opt_property == 'dip':
compound = utils.make_file_name(
population[poly_property_list.index(max_test)], poly_size)
polar_val = polar_list[poly_property_list.index(max_test)]
if opt_property == 'pol':
compound = utils.make_file_name(
population[poly_property_list.index(max_test)], poly_size)
dip_val = dip_list[poly_property_list.index(max_test)]
# create sorted monomer list with most freq first
gen2 = utils.sort_mono_indicies_list(mono_list)
# calculate Spearman correlation coefficient for begin and end sorted monomer lists
spear = stats.spearmanr(gen1[:n], gen2[:n])[0]
# spear_05 = stats.spearmanr(gen1[:n_05], gen2[:n_05])[0]
# spear_10 = stats.spearmanr(gen1[:n_10], gen2[:n_10])[0]
# spear_15 = stats.spearmanr(gen1[:n_15], gen2[:n_15])[0]
# capture monomer indexes and numerical sequence as strings for population file
analysis_file.write('%f, %f, %f, %f, \n' %
(min_test, max_test, avg_test, spear))
if opt_property == 'dip':
dip_polar_file.write('%s, %d, %f, %f, \n' %
(compound, gen_counter, max_test, polar_val))
if opt_property == 'pol':
polar_dip_file.write('%s, %d, %f, %f, \n' %
(compound, gen_counter, max_test, dip_val))
# spear_file.write('%d, %f, %f, %f, \n' %
# (gen_counter, spear_05, spear_10, spear_15))
# write polymer population to file
for polymer in population:
poly_name = utils.make_file_name(polymer, poly_size)
population_file.write('%s, ' % (poly_name))
population_file.write('\n')
for value in poly_property_list:
values_file.write('%f, ' % (value))
values_file.write('\n')
# keep track of number of successive generations meeting Spearman criterion
if spear > 0.92:
spear_counter += 1
else:
spear_counter = 0
# keep track of number of successive generations meeting property value convergence criterion
if max_test >= (max_init - max_init * 0.05) and max_test <= (
max_init + max_init * 0.05):
prop_value_counter += 1
else:
prop_value_counter = 0
# close all output files
analysis_file.close()
population_file.close()
values_file.close()
if opt_property == 'dip':
dip_polar_file.close()
if opt_property == 'pol':
polar_dip_file.close()
spear_file.close()
# make backup copies of output files
shutil.copy('gens_analysis.txt', 'gens_analysis_copy.txt')
shutil.copy('gens_population.txt', 'gens_population_copy.txt')
shutil.copy('gens_values.txt', 'gens_values_copy.txt')
if opt_property == 'dip':
shutil.copy('gens_dip_polar.txt', 'gens_dip_polar_copy.txt')
if opt_property == 'pol':
shutil.copy('gens_polar_dip.txt', 'gens_polar_dip_copy.txt')
shutil.copy('gens_spear.txt', 'gens_spear_copy.txt')
params = [
pop_size, poly_size, num_mono_species, opt_property, smiles_list,
sequence_list, mono_list, population, poly_property_list, n,
gen_counter, spear_counter, prop_value_counter
]
return (params)
def init_gen(pop_size, poly_size, num_mono_species, opt_property, perc,
smiles_list):
'''
Initializes parameter, creates population, and runs initial generation
Parameters
----------
pop_size: int
number of polymers in each generation
poly_size: int
number of monomers per polymer
num_mono_species: int
number of monomer species in each polymer (e.g. copolymer = 2)
opt_property: str
property being optimized
perc: float
percentage of number of monomers to compare with Spearman calculation
smiles_list: list
list of all possible monomer SMILES
Returns
-------
params: list (specific format)
[pop_size, poly_size, num_mono_species, opt_property, smiles_list, sequence_list, mono_list, population, poly_property_list, n, gen_counter, spear_counter, prop_value_counter]
'''
# create all possible numerical sequences for given number of monomer types
sequence_list = utils.find_sequences(num_mono_species)
n = int(len(smiles_list) * perc)
# n_05 = int(len(smiles_list) * .05)
# n_10 = int(len(smiles_list) * .10)
# n_15 = int(len(smiles_list) * .15)
# initialize generation counter
gen_counter = 1
# initialize convergence counter
spear_counter = 0
prop_value_counter = 0
# create monomer frequency list [(mono index 1, frequency), (mono index 2, frequency),...]
mono_list = []
for x in range(len(smiles_list)):
mono_list.append([x, 0])
# create inital population as list of polymers
population = []
population_str = []
counter = 0
while counter < pop_size:
# for polymer in range(pop_size):
temp_poly = []
# select sequence type for polymer
poly_seq = sequence_list[random.randint(0, len(sequence_list) - 1)]
temp_poly.append(poly_seq)
# select monomer types for polymer
for num in range(num_mono_species):
# randomly select a monomer index
poly_monomer = random.randint(0, len(smiles_list) - 1)
temp_poly.append(poly_monomer)
# increase frequency count for monomer in mono_list
mono_list[poly_monomer][1] += 1
# make SMILES string of polymer
temp_poly_str = utils.make_polymer_str(temp_poly, smiles_list,
poly_size)
# add polymer to population
# check for duplication - use str for comparison to avoid homopolymer, etc. type duplicates
if temp_poly_str in population_str:
pass
else:
population.append(temp_poly)
population_str.append(temp_poly_str)
counter += 1
# find initial population properties
if opt_property == 'mw':
# calculate polymer molecular weights
poly_property_list = find_poly_mw(population, poly_size, smiles_list)
elif opt_property == 'dip':
# initialize list of polarizabilities
polar_list = []
# calculate electronic properties for each polymer
elec_prop_list = find_elec_prop(population, poly_size, smiles_list)
poly_property_list = elec_prop_list[0]
polar_list = elec_prop_list[1]
elif opt_property == 'pol':
# initialize list of dipole moments
dip_list = []
# calculate electronic properties for each polymer
elec_prop_list = find_elec_prop(population, poly_size, smiles_list)
poly_property_list = elec_prop_list[1]
dip_list = elec_prop_list[0]
else:
print(
"Error: opt_property not recognized. trace:main:initial pop properties"
)
# set initial values for min, max, and avg polymer weights
min_test = min(poly_property_list)
max_test = max(poly_property_list)
avg_test = mean(poly_property_list)
if opt_property == 'dip':
compound = utils.make_file_name(
population[poly_property_list.index(max_test)], poly_size)
polar_val = polar_list[poly_property_list.index(max_test)]
if opt_property == 'pol':
compound = utils.make_file_name(
population[poly_property_list.index(max_test)], poly_size)
dip_val = dip_list[poly_property_list.index(max_test)]
# create new output files
analysis_file = open('gens_analysis.txt', 'w+')
population_file = open('gens_population.txt', 'w+')
values_file = open('gens_values.txt', 'w+')
if opt_property == 'dip':
dip_polar_file = open('gens_dip_polar.txt', 'w+')
if opt_property == 'pol':
polar_dip_file = open('gens_polar_dip.txt', 'w+')
spear_file = open('gens_spear.txt', 'w+')
# write files headers
analysis_file.write('min, max, avg, spearman, \n')
population_file.write('polymer populations \n')
values_file.write('%s values \n' % (opt_property))
if opt_property == 'dip':
dip_polar_file.write('compound, gen, dipole, polar \n')
if opt_property == 'pol':
polar_dip_file.write('compound, gen, polar, dip \n')
#spear_file.write('gen, spear_05, spear_10, spear_15 \n')
# capture initial population data
analysis_file.write('%f, %f, %f, n/a, \n' % (min_test, max_test, avg_test))
if opt_property == 'dip':
dip_polar_file.write('%s, %d, %f, %f, \n' %
(compound, 1, max_test, polar_val))
if opt_property == 'pol':
polar_dip_file.write('%s, %d, %f, %f, \n' %
(compound, 1, max_test, dip_val))
spear_file.write('1, n/a, n/a, n/a, \n')
# write polymer population to file
for polymer in population:
poly_name = utils.make_file_name(polymer, poly_size)
population_file.write('%s, ' % (poly_name))
population_file.write('\n')
for value in poly_property_list:
values_file.write('%f, ' % (value))
values_file.write('\n')
# close all output files
analysis_file.close()
population_file.close()
values_file.close()
if opt_property == 'dip':
dip_polar_file.close()
if opt_property == 'pol':
polar_dip_file.close()
spear_file.close()
# make backup copies of output files
shutil.copy('gens_analysis.txt', 'gens_analysis_copy.txt')
shutil.copy('gens_population.txt', 'gens_population_copy.txt')
shutil.copy('gens_values.txt', 'gens_values_copy.txt')
if opt_property == 'dip':
shutil.copy('gens_dip_polar.txt', 'gens_dip_polar_copy.txt')
if opt_property == 'pol':
shutil.copy('gens_polar_dip.txt', 'gens_polar_dip_copy.txt')
shutil.copy('gens_spear.txt', 'gens_spear_copy.txt')
params = [
pop_size, poly_size, num_mono_species, opt_property, smiles_list,
sequence_list, mono_list, population, poly_property_list, n,
gen_counter, spear_counter, prop_value_counter
]
return (params)
def find_elec_prop(population, poly_size, smiles_list):
'''
Calculates dipole moment and polarizability of each polymer in population
TODO: add dipole tensor functionality
TODO: update parser to catch failures/errors in output file
Parameters
---------
population: list
list of polymers in population
poly_size: int
number of monomers per polymer
smiles_list: list
list of all possible monomer SMILES
Returns
-------
elec_prop_lists: list
nested list of [list of polymer dipole moments, list of polymer polarizabilities]
'''
poly_polar_list = []
poly_dipole_list = []
# run xTB geometry optimization
#nproc = 8
for polymer in population:
run_geo_opt(polymer, poly_size, smiles_list)
# parse xTB output files
for polymer in population:
# make file name string w/ convention monoIdx1_monoIdx2_fullNumerSequence
file_name = utils.make_file_name(polymer, poly_size)
# count number of successful parsed properties
num_succ_reads = 0
# check for xTB failures
if 'FAILED!' in open('output/%s.out' % (file_name)).read():
# move output file to 'failed' directory
move_fail_file = subprocess.call(
'(mv output/%s.out failed/%s.out)' % (file_name, file_name),
shell=True)
# note failure by filling property lists with dummy values
poly_polar_list.append(-10)
poly_dipole_list.append(-10)
# if xTB successful, parse output file for static polarizability and dipole moment
else:
read_output = open('output/%s.out' % (file_name), 'r')
for line in read_output:
# create list of tokens in line
tokens = line.split()
if line.startswith(" Mol. α(0)"):
temp_polar = float(tokens[4])
poly_polar_list.append(temp_polar)
num_succ_reads += 1
elif line.startswith(" full:"):
# dipole tensor - STILL A LIST OF STRINGS (not floats)
# TODO: add tensor functionality later
dipole_line = tokens
temp_dipole = float(tokens[4])
poly_dipole_list.append(temp_dipole)
num_succ_reads += 1
# break inner for loop to avoid overwriting with other lines starting with "full"
break
read_output.close()
# This is a catch to move files to the failed folder if polarizability
# .. and dipole are not parsed.
if num_succ_reads != 2:
poly_polar_list.append(-10)
poly_dipole_list.append(-10)
move_fail_file = subprocess.call(
'(mv output/%s.out failed/%s.out)' % (file_name, file_name),
shell=True)
# reset the number of successful reads
num_succ_reads = 0
# make nested list of dipole moment and polarizability lists
elec_prop_lists = [poly_dipole_list, poly_polar_list]
return elec_prop_lists
def main():
param = {
'N_time_step': 100,
'N_quench': 0,
'Ti': 0.04,
'action_set': 0,
'hx_initial_state': -2.0,
'hx_final_state': 2.0,
'delta_t': 0.001,
'hx_i': -4.0,
'RL_CONSTRAINT': True,
'L': 6,
'J': 1.00,
'hz': 1.0,
'symmetrize': False
}
file_name = ut.make_file_name(param)
res = ut.gather_data(param, "../data/")
print(compute_observable.Ed_Ad_OP(res['h_protocol'], 4))
plotting.protocol(range(100), res['h_protocol'][0])
#plotting.protocol(range(100),res['h_protocol'][1])
#print(res['fid'])
#print(res.keys())
print(file_name)
#with open('
exit()
import os
#===========================================================================
# pca=PCA(n_components=2)
# param['N_time_step']=10
# dc=ut.gather_data(param,'../data/')
# pca.fit(dc['h_protocol']/4.)
# X=pca.transform(dc['h_protocol']/4.)
#
# plt.scatter(X[:,0],X[:,1])
# plt.title('PCA, $t=0.1$, continuous protocol')
# plt.savefig("PCA_AS2_t-0p1.pdf")
# plt.show()
# exit()
#===========================================================================
#===========================================================================
# dataBB8=[]
# param['action_set']=0
# param['N_time_step']=60
#
# param['delta_t']=0.5/60.
# dc=ut.gather_data(param,'../data/')
# pca=PCA(n_components=2)
# pca.fit(dc['h_protocol']/4.)
# print(pca.explained_variance_ratio_)
# exit()
#
# param['delta_t']=3.0/60.
# dc=ut.gather_data(param,'../data/')
# X=pca.transform(dc['h_protocol']/4.)
#
# title='PCA$_{50}$, $t=3.0$, continuous protocol, nStep$=60$'
# out_file="PCA_AS0_t-3p0_nStep-60.pdf"
# plotting.visne_2D(X[:,0],X[:,1],dc['fid'],zlabel="Fidelity",out_file=out_file,title=title,show=True,xlabel='PCA-1',ylabel='PCA-2')
#
#===========================================================================
#exit()
#plt.scatter(X[:,0],X[:,1])
#plt.title('PCA$_{50}$, $t=1.5$, continuous protocol, nStep$=60$')
#plt.savefig("PCA_AS0_t-0p8_nStep-60.pdf")
#plt.show()
#exit()
# exit()
#===========================================================================
# param['N_time_step']=2
# param['action_set']=0
# dc=ut.gather_data(param,'../data/')
# print(dc['h_protocol'])
# exit()
# dataBB8=[]
#===========================================================================
#===============================================================================
#
# param['action_set']=0
# param['N_time_step']=60
# param['delta_t']=0.5/60
#
# dc=ut.gather_data(param,'../data/')
#
# protocols=dc['h_protocol']
# #print(np.shape(dc['h_protocol']))
# sort_f=np.argsort(dc['fid'])[::-1]
#
# print(sort_f[0])
#
# #protocols[sort_f[0]]
#
# best_prot=protocols[sort_f[0:10]]
# x=np.array(range(60))*1.0/60
# #print(best_prot.reshape)
# #print(x.shape)
# #print(np.array(range(60))*0.1/60)
# #print(best_prot)
# #print(np.shape(best_prot))
# #print(np.shape(np.arange(0.1,3.05,0.1)*0.05))
#
# plotting.protocol(protocols[:2],x,labels=dc['fid'][:2],show=True)
#
# exit()
#
#
#===============================================================================
param['N_time_step'] = 60
param['action_set'] = 0
dataBB8 = []
compTime = []
x = []
for t in np.arange(0.1, 3.05, 0.1):
dt = t / param['N_time_step']
param['delta_t'] = dt
# Changed it to be returning False if file is not found ...
dc = ut.gather_data(param, '../data/')
if dc is not False:
eaop = compute_observable.Ed_Ad_OP(dc['h_protocol'], 4.0)
print(t, eaop, dc['fid'].shape, '\t', np.mean(dc['n_fid']))
compTime.append(np.mean(dc['n_fid']))
dataBB8.append(eaop)
x.append(t)
else:
print("Data not available for %.3f" % dt)
y = compTime
plotting.observable(y,
x,
title='Depth of search for bang-bang protocol',
ylabel='\# of fidelity evaluations',
xlabel='$T$',
marker="-",
labels=['Obtained time (SGD)'])
exit()
#===========================================================================
# param['action_set']=0
# param['delta_t']=0.01
#===========================================================================
#===========================================================================
# for i in range(2,300,4):
# param['N_time_step']=i
# is_there,dc=ut.gather_data(param,'../data/')
# if is_there:
# eaop=compute_observable.Ed_Ad_OP(dc['h_protocol'],4.0)
# print(i,eaop,dc['fid'].shape,'\t',np.mean(dc['n_fid']))
# compTime.append(np.mean(dc['n_fid']))
# dataBB8.append(eaop)
# x.append(i)
# else:
# print("Data not available for %i"%i)
#
#===========================================================================
#===========================================================================
# param['N_time_step']=150
# is_there,dc=ut.gather_data(param,'../data/')
# x=np.arange(0,150*0.01,0.01)
# plotting.protocol(dc['h_protocol'][:3],x,labels=dc['fid'][:3],show=True)
# exit()
# #x=np.array(range(2,300,4))*0.01
#===========================================================================
param['action_set'] = 0
param['delta_t'] = 0.01
mean_fid_BB = []
h_protocol_BB = {}
fid_BB = {}
n_fid_BB = []
x = []
sigma_fid = []
EA_OP = []
for i in range(2, 300, 4):
param['N_time_step'] = i
data_is_available, dc = ut.gather_data(param, '../data/')
if data_is_available:
mean_fid_BB.append(np.mean(dc['fid']))
sigma_fid.append(np.std(dc['fid']))
fid_BB[i] = dc['fid']
EA_OP.append(compute_observable.Ed_Ad_OP(dc['h_protocol'], 4.0))
h_protocol_BB[i] = dc['h_protocol']
n_fid_BB.append(np.mean(dc['n_fid']))
x.append(i * param['delta_t'])
#print(fid_BB[130])
#mean=np.mean(fid_BB[130])
#sns.distplot(fid_BB[130],bins=np.linspace(mean-0.005,mean+0.005,100))
#plt.tick_params(labelleft='off')
#plt.show()
x = np.array(x)
y = [
n / (x[i] / param['delta_t'])
for n, i in zip(n_fid_BB, range(len(n_fid_BB)))
]
plotting.observable(y,
x,
title='Depth of search for bang-bang protocol',
ylabel='(\# of fidelity evaluations)/$N$',
xlabel='$T$',
marker="-",
labels=['Minimum time', 'Obtained time (SGD)'])
#plotting.protocol(h_protocol_BB[130][20:25],np.arange(0,130,1)*param['delta_t'])
exit()
#pca.fit()
#===========================================================================
# dataCONT=[]
# for t in range(2,300,4):
# print(t)
# param['N_time_step']=t
# dc=ut.gather_data(param,'../data/')
# #print(dc['h_protocol'].shape)
# eaop=compute_observable.Ed_Ad_OP(dc['h_protocol'],4.0)
# print(eaop)
# dataCONT.append(eaop)
#
# file="../data/EAOP_"+ut.make_file_name(param)
# with open(file,'wb') as f:
# pickle.dump(dataCONT,f);f.close();
#
# exit()
#
#===========================================================================
#===========================================================================
# param['action_set']=0
# dataBB8=[]
# for t in range(2,300,4):
# print(t)
# param['N_time_step']=t
# dc=ut.gather_data(param,'../data/')
# eaop=compute_observable.Ed_Ad_OP(dc['h_protocol'],4.0)
# print(eaop)
# #print(dc['h_protocol'].shape)
# dataBB8.append(eaop)
#
# file="../data/EAOP_"+ut.make_file_name(param)
# with open(file,'wb') as f:
# pickle.dump(dataBB8,f);f.close();
#
# exit()
#===========================================================================
#===========================================================================
# param['N_time_step']=298
# param['action_set']=0
# file="../data/EAOP_"+ut.make_file_name(param)
# with open(file,'rb') as f:
# dataBB8=pickle.load(f);f.close();
#
# param['action_set']=2
# f="../data/EAOP_"+ut.make_file_name(param)
# with open(f,'rb') as file:
# dataCONT=pickle.load(file);
#
# time_axis=np.array(range(2,300,4))*0.01
# title="Edward-Anderson parameter ($n=400$) vs. evolution time for SGD\n with the different action protocols ($L=1$)"
# plotting.observable([dataBB8,dataCONT],[time_axis,time_axis],title=title,
# out_file="SGD_EAOPvsT_AS0-2.pdf",show=True,
# ylabel="$q_{EA}$",xlabel="$t$",labels=['bang-bang8','continuous'])
#===========================================================================
#===========================================================================
# param['N_time_step']=250
# dc=ut.gather_data(param,'../data/')
# sns.distplot(dc['fid'],kde=False,label='$t=%.3f$'%(param['N_time_step']*0.01))
# plt.legend(loc='best')
# plt.savefig('SGD_hist_fid_t2p5.pdf')
# plt.show()
# exit()
#===========================================================================
#===========================================================================
# title="Fidelity ($n=400$) vs. evolution time for SGD\n with the different action protocols ($L=1$)"
# plotting.observable(np.array(data),np.array(range(2,300,4))*0.01,title=title,
# out_file="SGD_FvsT_AS2.pdf",show=True,
# ylabel="$F$",xlabel="$t$",labels=['continuous'])
#
#===========================================================================
exit()
def b2(n10,w=10):
x = np.array(list(np.binary_repr(n10, width=w)),dtype=np.float)
x[x > 0.5] = 4.
x[x < 0.5] = -4.
return x
par=default_parameters()
par['symmetrize']=False
par['L']=6
best_fid=0
best_fid_list=[]
for n in range(10,405,10):
par['N_time_step'] = n
file=make_file_name(par)
with open('data/'+file, 'rb') as f:
data = pickle.load(f)
for d in data[1]:
if d[1] > best_fid:
best_fid = d[1]
best_fid_list.append(best_fid)
np.savetxt('out.txt',best_fid_list)
#print(data)
exit()
h=data[0][1]
dt=0.015
t=np.arange(0,3.0,dt)
plotting.protocol(t,h)
def main():
ut.check_sys_arg(sys.argv)
global action_set,hx_discrete,hx_max#,FIX_NUMBER_FID_EVAL
continuous=[0.01,0.05,0.1,0.2,0.5,1.,2.,3.,4.,8.]
action_set_name=["bang-bang8","continuous-pos","continuous"]
action_set_arrays=[
np.array([-8.0,0.,8.]),
np.array(continuous,dtype=np.float32),
np.array([-c for c in continuous]+[0]+continuous,dtype=np.float32)
]
all_action_sets=dict(zip(action_set_name,action_set_arrays))
"""
Parameters
L: system size
J: Jzz interaction
hz: longitudinal field
hx_i: initial tranverse field coupling
hx_initial_state: initial state transverse field
hx_final_state: final state transverse field
Ti: initial temperature for annealing
N_quench: number of quenches (i.e. no. of time temperature is quenched to reach exactly T=0)
N_time_step: number of time steps
action_set: array of possible actions
outfile_name: file where data is being dumped (via pickle)
delta_t: time scale
N_restart: number of restart for the annealing
verbose: If you want the program to print to screen the progress
symmetrize_protocol: Wether or not to work in the symmetrized sector of protocols
hx_max : maximum hx field (the annealer can go between -hx_max and hx_max
FIX_NUMBER_FID_EVAL: decide wether you want to fix the maximum number of fidelity evaluations (deprecated)
RL_CONSTRAINT: use reinforcement learning constraints or not
fidelity_fast: prepcompute exponential matrices and runs fast_Fidelity() instead of Fidelity()
"""
#----------------------------------------
# DEFAULT PARAMETERS
J = 1.0 # zz interaction
hz = 1.0 #0.9045/0.809 #1.0 # hz field
hx_i = -4.0 # -1.0 # initial hx coupling
act_set_name='bang-bang8'
Ti=0.04 # initial temperature (for annealing)
L = 10 # system size
hx_initial_state= -2.0 # initial state
hx_final_state = 2.0 #+1.0 # final hx coupling
N_quench=10
N_time_step=40
outfile_name='first_test.pkl'
action_set=all_action_sets['bang-bang8']
delta_t=0.05
N_restart=4
symmetrize_protocol=True
hx_max=4
h_set=compute_h_set(hx_i,hx_max)
RL_CONSTRAINT=True
verbose=True
fidelity_fast=True
#----------------------------------------
if len(sys.argv)>1:
"""
if len(sys.argv) > 1 : run from command line -- check command line for parameters
"""
argv=ut.read_command_line_arg(sys.argv,all_action_sets)
L=argv[0]
hx_initial_state=argv[1]
hx_final_state=argv[2]
N_quench=argv[3]
N_time_step=argv[4]
action_set=argv[5]
outfile_name=argv[6]
delta_t=argv[7]
N_restart=argv[8]
verbose=argv[9]
act_set_name=argv[10]
symmetrize_protocol=argv[11]
print("-------------------- > Parameters < --------------------")
print("L \t\t\t %i\nJ \t\t\t %.3f\nhz \t\t\t %.3f\nhx(t=0) \t\t %.3f\nhx_max \t\t\t %.3f "%(L,J,hz,hx_i,hx_max))
print("hx_initial_state \t %.2f\nhx_final_state \t\t %.2f"%(hx_initial_state,hx_final_state))
print("N_quench \t\t %i\ndelta_t \t\t %.2f\nN_restart \t\t %i"%(N_quench,delta_t,N_restart))
print("N_time_step \t\t %i"%N_time_step)
print("Total_time \t\t %.2f"%(N_time_step*delta_t))
print("Output file \t\t %s"%('data/'+outfile_name))
print("Action_set \t <- \t %s"%np.round(action_set,3))
print("# of possible actions \t %i"%len(action_set))
print("Using RL constraints \t %s"%str(RL_CONSTRAINT))
print("Symmetrizing protocols \t %s"%str(symmetrize_protocol))
print("Fidelity MODE \t\t %s"%('fast' if fidelity_fast else 'standard'))
param={'J':J,'hz':hz,'hx':hx_i} # Hamiltonian kwargs
hx_discrete=[0]*N_time_step # dynamical part at every time step (initiaze to zero everywhere)
# full system hamiltonian
H,_ = Hamiltonian.Hamiltonian(L,fct=hx_vs_t,**param)
# calculate initial and final states
hx_discrete[0]=hx_initial_state # just a trick to get initial state
_, psi_i = H.eigsh(time=0,k=1,which='SA')
hx_discrete[0]=hx_final_state # just a trick to get final state
_, psi_target = H.eigsh(time=0,k=1,which='SA')
hx_discrete[0]=0
print("Initial overlap is \t %.5f"%(abs(np.sum(np.conj(psi_i)*psi_target))**2))
# simulated annealing kwargs:
param_SA={'Ti':Ti,
'psi_i':psi_i,'H':H,'N_time_step':N_time_step,
'delta_t':delta_t,'psi_target':psi_target,
'hx_i':hx_i,'N_quench':N_quench,'RL_CONSTRAINT':RL_CONSTRAINT,
'verbose':verbose,'hx_initial_state':hx_initial_state,'hx_final_state':hx_final_state,
'L':L,'J':J,'hz':hz,'action_set':action_set_name.index(act_set_name),
'fidelity_fast':fidelity_fast,'symmetrize':symmetrize_protocol
}
if param_SA['fidelity_fast'] :
print("\nPrecomputing evolution matrices ...")
start=time.time()
precompute_expmatrix(param_SA, h_set, H)
print("Done in %.4f seconds"%(time.time()-start))
if outfile_name=="auto": outfile_name=ut.make_file_name(param_SA)
to_save_par=['Ti','psi_i','N_time_step',
'delta_t','psi_target','hx_i','N_quench','RL_CONSTRAINT',
'hx_initial_state','hx_final_state','L','J','hz','action_set',
'symmetrize'
]
file_content=ut.read_current_results('data/%s'%outfile_name)
# Read current data if it exists
if file_content :
dict_to_save_parameters, all_results = file_content
N_current_restart = len(all_results)
print("Data with %i samples available !" % N_current_restart)
else :
dict_to_save_parameters = dict(zip(to_save_par,[param_SA[p] for p in to_save_par]))
all_results=[]
N_current_restart = 0
#print(N_current_restart," ",N_restart)
for it in range(N_current_restart, N_restart):
print("\n\n-----------> Starting new iteration <-----------")
start_time=time.time()
count_fid_eval,best_fid,best_action_protocol,best_hx_discrete = simulate_anneal(param_SA)
result=[count_fid_eval,best_fid,best_action_protocol,best_hx_discrete]
print("\n----------> RESULT FOR ANNEALING NO %i <-------------"%(it+1))
print("Number of fidelity eval \t%i"%count_fid_eval)
print("Best fidelity \t\t\t%.4f"%best_fid)
print("Best hx_protocol\t\t",list(best_hx_discrete))
if L > 1:
_,E,delta_E,Sd,Sent = MB_observables(best_hx_discrete, param_SA, matrix_dict, fin_vals=True)
result = result + [E, delta_E, Sd, Sent] # Appending Energy, Energy fluctuations, Diag. entropy, Ent. entropy
all_results.append(result)
with open('data/%s'%outfile_name,'wb') as pkl_file:
## Here read first then save, stop if reached quota
pickle.dump([dict_to_save_parameters,all_results],pkl_file);pkl_file.close()
print("Saved iteration --> %i to %s"%(it,'data/%s'%outfile_name))
print("Iteration run time --> %.2f s"%(time.time()-start_time))
print("\n Thank you and goodbye !")