def all_train_and_test_from_outside():
os.system('cp ../data_prescreening/input.json ./')
file_json = 'input.json'
xxx_input = sub_inp_json.load_json(file_json)
n_traj_select_train = int(xxx_input['n_traj_select_train'])
n_x_dim = int(xxx_input['n_x_dim'])
n_y_dim = int(xxx_input['n_y_dim'])
label_x_descriptor = int(xxx_input['label_x_descriptor'])
n_train_geom = int(xxx_input['n_train'])
# Copy geometries and energies
curr_dir = os.getcwd()
# -----------------------------------------------------
sub_copy_data.copy_and_check_from_outside(n_traj_select_train)
os.chdir(curr_dir)
# Collect all data
# -----------------------------------------------------
sub_collect_x_y.collect_all_from_file()
os.chdir(curr_dir)
# ----------------------------------------------------------------
filename = descriptor_file(label_x_descriptor)
sub_select_train_test.get_train_test_from_outside(n_train_geom, filename,
n_x_dim, n_y_dim)
os.chdir(curr_dir)
def make():
curr_path = os.getcwd()
work_path = curr_path + "/all"
inp = json.load_json('inp.json')
i_dimension = int(inp['mds_dimension'].encode('utf-8'))
job = inp['job_select']
os.chdir(work_path)
classical_mds(i_dimension,job)
os.chdir(curr_path)
def make():
curr_path = os.getcwd()
work_path = curr_path + "/all"
inp = json.load_json('inp.json')
distance_cutoff = float(inp['rmsd_cutoff'].encode('utf-8'))
n_dimension = int(inp['mds_dimension'].encode('utf-8'))
os.chdir(work_path)
analy_result(n_dimension, distance_cutoff)
os.chdir(curr_path)
def Exch(coord):
inp = json.load_json('inp.json')
exch = []
exch = eval(inp['exch_matrix'].encode('utf-8'))
list1 = inp['exch_list']
natom = inp['n_atom']
list2 = []
change_save = []
change_save = exch_atom(coord, exch, list1, natom)
return change_save
def make_first():
inp = json.load_json('inp.json')
n_geom = int(inp['n_geom'])
n_atom = int(inp['n_atom'])
npro = int(inp['n_pro'])
curr_path = os.getcwd()
dir_path = curr_path + '/all/'
command = 'cp inp.json ' + dir_path
os.system(command)
rmsd_many(n_geom, n_atom, npro)
def make_second(id, workdir):
n_geom = id
inp = json.load_json('inp.json')
n_atom = int(inp['n_atom'])
npro = int(inp['n_pro'])
dir_path = workdir
command = 'cp inp.json ' + dir_path
os.system(command)
os.chdir(dir_path)
rmsd_many(n_geom, n_atom, npro)
def __init__(self, coord1, coord2):
inp = json.load_json('inp.json')
self.charality = inp['charality']
self.exchange = inp['exchange']
self.exchnu = None
self.atom = inp['n_atom']
self.coord1 = coord1
self.coord2 = coord2
self.mina = None
self.geom_mina = None
self.rmsd_list = []
self.num = 0
def __init__(self):
file_json = 'input.json'
xxx_input = sub_inp_json.load_json(file_json)
self.rescale = xxx_input['rescale']
self.n_x_dim = int(xxx_input['n_x_dim'])
self.n_y_dim = int(xxx_input['n_y_dim'])
self.para_gamma = xxx_input['para_gamma']
self.para_alpha = xxx_input['para_alpha']
self.para_kernel = xxx_input['para_kernel']
self.para_gamma = self.para_gamma[1:-1]
self.para_gamma = self.para_gamma.split(',')
self.para_alpha = self.para_alpha[1:-1]
self.para_alpha = self.para_alpha.split(',')
self.npro_train = int(xxx_input['npro_train'])
def make_first():
inp = json.load_json('inp.json')
npro = int(inp['n_pro'])
ntraj = int(inp['n_traj'])
dis = np.arange(ntraj * ntraj).reshape(ntraj, ntraj)
dis = dis.astype(float)
print dis
for i in range(ntraj):
for j in range(ntraj):
print i, j
path1 = i + 1
path2 = j + 1
curr_path = os.getcwd()
dis[i, j] = rmsd_many(path1, path2, npro)
print dis
np.savetxt('similarity.dat', dis)
def __init__(self, dir_fit_dat, dir_all_traj, dir_result):
self.home_dir = os.getcwd()
self.dir_fit_dat = dir_fit_dat
self.dir_all_traj = dir_all_traj
self.dir_result = dir_result
com = 'cp ' + dir_fit_dat + '/input.json ./'
os.system(com)
file_json = 'input.json'
xxx_input = sub_inp_json.load_json(file_json)
self.n_atom = int(xxx_input['n_atom'])
self.n_traj = int(xxx_input['n_traj'])
self.n_x_dim = int(xxx_input['n_x_dim'])
self.n_y_dim = int(xxx_input['n_y_dim'])
self.n_state = self.n_y_dim
self.para_gamma = xxx_input['para_gamma'][1:-1].split(',')
self.para_alpha = xxx_input['para_alpha'][1:-1].split(',')
self.para_kernel = xxx_input['para_kernel']
self.npro_train = int(xxx_input['npro_train'])
self.fit_files = ['fitting_para.dat', 'x_train.dat', 'y_train.dat', 'x_range.dat']
gamma = self.para_gamma[0]
alpha = self.para_alpha[0]
i_state = 0
dir_gamma = '/fit_result_kkr_gamma_' + str(gamma) + \
'_alpha_' + str(alpha) + \
'_S' + str(i_state)
tmp_dir = self.dir_fit_dat + dir_gamma
list_tmp = os.listdir(tmp_dir)
for ffile in list_tmp:
m = re.match('kkr.pkl', ffile)
if m:
self.fit_files.append(ffile)
self.filename_pe_dyn_gather = 'pe_time_aferselect.out'
self.filename_geom_dyn_sample = 'geom.xyz'
self.filename_grad_dyn_sample = 'grad_dyn.xyz'
self.filename_grad_kkr_sample = 'gradient_1d.xyz'
self.filename_grad_kkr_gather = 'grad_kkr.xyz'
self.filename_grad_cmp_sample = '/grad_cmp.dat'
self.filename_grad_cmp_gather = '/grad_cmp.dat'
def __init__(self):
self.inp = json.load_json('inp.json')
self.rmsd_matrix = []
self.savelist = []
def kkr_single_geom_all():
kkrname = "kkr.json"
xxx_input = sub_inp_json.load_json(kkrname)
n_x_dim = int(xxx_input['n_x_dim'])
n_y_dim = int(xxx_input['n_y_dim'])
label_x_descriptor = int(xxx_input['label_x_descriptor'])
para_kernel = xxx_input['para_kernel']
rescale = xxx_input['rescale']
label_grad = xxx_input['label_grad']
para_alpha = float(xxx_input['para_alpha'])
para_gamma = float(xxx_input['para_gamma'])
energy_zero = float(xxx_input['energy_zero'])
curr_dir = os.getcwd()
kkr_path = './kkr'
x_train = np.loadtxt('./kkr/x_train.dat')
for i_y_dim in range(n_y_dim):
work_path = kkr_path + '/' + str(i_y_dim + 1)
os.chdir(work_path)
os.system('rm -rf coulomb_input.dat distance_matrix.dat gradient_1d.xyz x_inversed_input.dat')
os.system(
'rm -rf coulomb_matrix.dat energy_gradient_col.dat geom.xyz gradient.xyz standard.xyz x_input.dat x_pre.dat')
os.system('cp ../../geom.xyz .')
fit_path = './'
work_path = './'
kkr_single_all = kkr_single_all_step(n_x_dim, n_y_dim, x_train, para_kernel, para_gamma, para_alpha, fit_path,
work_path,
rescale, label_grad, label_x_descriptor)
kkr_single_all.kkr_all_step()
os.chdir(curr_dir)
file_kkr_result = open('qm_results.dat', 'w')
file_geom = open('geom.xyz', 'r')
n_atom = int(file_geom.readline())
file_geom.readline()
file_kkr_result.write(' ' + str(n_atom) + '\n')
file_kkr_result.write(' The coordinates\n')
for i_atom in range(n_atom):
line_text = file_geom.readline().split()
line_text[1] = float(line_text[1]) / 0.529
line_text[2] = float(line_text[2]) / 0.529
line_text[3] = float(line_text[3]) / 0.529
file_kkr_result.write(
str(line_text[0]) + ' ' + str(line_text[1]) + ' ' + str(line_text[2]) + ' ' + str(line_text[3]) + '\n')
file_geom.close()
file_kkr_result.write(' Energy of electronic states\n')
for i_y_dim in range(n_y_dim):
kkr_file = kkr_path + '/' + str(i_y_dim + 1) + '/' + 'gradient.xyz'
file_kkr_pre = open(kkr_file, 'r')
file_kkr_pre.readline()
file_kkr_pre.readline()
for i_atom in range(n_atom):
file_kkr_pre.readline()
line_text = file_kkr_pre.readline().split()
kkr_energy = energy_zero + float(line_text[3])
file_kkr_result.write(str(kkr_energy) + '\n')
file_kkr_pre.close()
file_kkr_result.write('Gradient of electronic states\n')
for i_y_dim in range(n_y_dim):
file_kkr_result.write(' State: ' + str(i_y_dim + 1) + '\n')
kkr_file = kkr_path + '/' + str(i_y_dim + 1) + '/' + 'gradient.xyz'
file_kkr_pre = open(kkr_file, 'r')
file_kkr_pre.readline()
file_kkr_pre.readline()
for i_atom in range(n_atom):
file_kkr_pre.readline()
file_kkr_pre.readline()
file_kkr_pre.readline()
file_kkr_pre.readline()
for i_atom in range(n_atom):
file_kkr_result.write(file_kkr_pre.readline())
file_kkr_pre.close()
file_kkr_result.close()
#! /usr/bin/env python
import rmsd_analys
import mds_cla
import mds_analys
import sub_inp_json as json
import os
import shutil
inp = json.load_json('inp.json')
inp['job_select'] = raw_input(
"which job do u choose,classical or isomap(classical/isomap):")
inp['rmsd_cutoff'] = raw_input("Input the rmsd_cutoff value:")
if inp['job_select'] == 'isomap':
inp['mds_cutoff'] = raw_input("Input the mds_cutoff value:")
inp['mds_dimension'] = raw_input("Choose mds dimension:")
json.dump_json('inp.json', inp)
if inp['job_select'] == 'isomap':
file_name = inp['job_select'] + '_rmsdcut_' + inp[
'rmsd_cutoff'] + '_mdscut_' + inp['mds_cutoff']
if inp['job_select'] == 'classical':
file_name = inp['job_select'] + '_rmsdcut_' + inp['rmsd_cutoff']
curr_dir = os.getcwd()
workdir = curr_dir + '/' + file_name
if os.path.exists(workdir):
shutil.rmtree(workdir)
os.mkdir(workdir)
command1 = 'cp -r all ' + workdir
command2 = 'cp inp.json ' + workdir
os.system(command1)
os.system(command2)
def additional_test():
os.system('cp ../train_and_test/input.json ./')
file_json = 'input.json'
xxx_input = sub_inp_json.load_json(file_json)
n_traj_test = int(xxx_input['n_predict_traj'])
n_x_dim = int(xxx_input['n_x_dim'])
n_y_dim = int(xxx_input['n_y_dim'])
label_x_descriptor = int(xxx_input['label_x_descriptor'])
para_gamma = xxx_input['para_gamma']
para_alpha = xxx_input['para_alpha']
para_gamma = para_gamma[1:-1]
para_gamma = para_gamma.split(',')
para_alpha = para_alpha[1:-1]
para_alpha = para_alpha.split(',')
para_kernel = xxx_input['para_kernel']
rescale = xxx_input['rescale']
npro_train = int(xxx_input['npro_train'])
print("Copy add geometries for testing!")
curr_dir = os.getcwd()
sub_copy_additional_test_data.copy_geom_energy(n_traj_test)
os.chdir(curr_dir)
print("collect all geometries for testing!")
# Collect all data
# -----------------------------------------------------
sub_collect_x_y.collect_all_traj(n_traj_test)
os.chdir(curr_dir)
# ----------------------------------------------------------------
filename = descriptor_file(label_x_descriptor)
construct_data_input(n_traj_test, filename, n_x_dim, n_y_dim)
os.chdir(curr_dir)
# Additional Test
if npro_train > 1:
pool = multiprocessing.Pool(processes=npro_train)
print("Start work on test")
for para_gamma1 in para_gamma:
for para_alpha1 in para_alpha:
for i_state in range(n_y_dim):
pool.apply_async(test_single, (
para_gamma1,
para_alpha1,
i_state,
n_traj_test,
n_x_dim,
para_kernel,
rescale,
))
pool.close()
pool.join()
elif npro_train == 1:
for para_gamma1 in para_gamma:
for para_alpha1 in para_alpha:
for i_state in range(n_y_dim):
test_single(para_gamma1, para_alpha1, i_state, n_traj_test,
n_x_dim, para_kernel, rescale)
plot_dir = 'plot_result'
if os.path.exists(plot_dir):
command1 = 'rm -r ' + str(plot_dir)
os.system(command1)
os.system('mkdir plot_result')
for para_gamma1 in para_gamma:
for para_alpha1 in para_alpha:
plot_many_pes_time(n_traj_test, n_y_dim, para_gamma1, para_alpha1)
os.chdir(curr_dir)