import numpy as np
import sys, os
from pbc import PBC
# Initialize periodic boundry condition object
pbc_i = PBC()
# Print lattice vectors
pbc_i.print_basis()
npos_i = []
npos_i.append(np.array([25.0, 25.0, 25.0], dtype="float64"))
npos_i.append(np.array([5.0, 75.0, 25.0], dtype="float64"))
npos_j = []
npos_j.append(np.array([-10.0, -15.0, 0.0], dtype="float64"))
npos_j.append(np.array([-25.0, -90.0, -45.0], dtype="float64"))
npos_ij, nd_ij = pbc_i.delta_npos(npos_i, npos_j)
for n in range(len(npos_i)):
pos_i = npos_i[n]
print " pos_i %d [ %f %f %f ] \n" % (n + 1, pos_i[0], pos_i[1], pos_i[2])
for n in range(len(npos_j)):
pos_j = npos_j[n]
print " pos_j %d [ %f %f %f ] \n" % (n + 1, pos_j[0], pos_j[1], pos_j[2])
for n in range(len(npos_i)):
for m in range(len(npos_j)):
pos_ij = npos_ij[n][m]
print " pos_ij %d %d [ %f %f %f ] | %f | \n" % (n + 1, m + 1, pos_ij[0], pos_ij[1], pos_ij[2], nd_ij[n][m])
def main():
print out_line
mod_name = "pbc"
term_width=80
orig_stdout = sys.stdout
test_list = []
command='import numpy as np'
tag='importnumpy'
rshift=len(tag)+len(command)
try:
import numpy as np
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='from pbc import PBC'
tag='importPBC'
rshift=len(tag)+len(command)
try:
from pbc import PBC
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i = PBC'
tag='intializePBC'
rshift=len(tag)+len(command)
try:
pbc_i = PBC()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.return_basis()'
tag='return_basis_2'
rshift=len(tag)+len(command)
try:
basis_i = pbc_i.return_basis()
f = open('%s.test'%(tag), 'w')
for i in range(pbc_i.lat.d):
for j in range(pbc_i.lat.d):
f.write(" basis_i [%d][%d] = %g \n"%(i,j,basis_i[i][j]))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.set_basis()'
tag='set_basis_1'
rshift=len(tag)+len(command)
try:
basis_i = pbc_i.return_basis()
f = open('%s.test'%(tag), 'w')
for i in range(pbc_i.lat.d):
for j in range(pbc_i.lat.d):
f.write(" basis_o [%d][%d] = %g \n"%(i,j,basis_i[i][j]))
basis_i[0,0]=150.0
basis_i[1,1]=150.0
basis_i[2,2]=150.0
pbc_i.set_basis(basis_i)
for i in range(pbc_i.lat.d):
for j in range(pbc_i.lat.d):
f.write(" basis_i [%d][%d] = %g \n"%(i,j,basis_i[i][j]))
f.write(" a = %g \n"%(pbc_i.lat.a))
f.write(" b = %g \n"%(pbc_i.lat.b))
f.write(" c = %g \n"%(pbc_i.lat.c))
f.write(" alpha = %g \n"%(pbc_i.lat.alpha))
f.write(" gamma = %g \n"%(pbc_i.lat.gamma))
f.write(" beta = %g \n"%(pbc_i.lat.beta))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.find_Bravais()'
tag='find_Bravais_1'
rshift=len(tag)+len(command)
try:
Bravais_numb = pbc_i.find_Bravais()
Bravais_type = pbc_i.return_Bravais()
f = open('%s.test'%(tag), 'w')
f.write(" Bravais %s [%d] \n"%(Bravais_type,Bravais_numb))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.delta_npos()'
tag='delta_npos_1'
rshift=len(tag)+len(command)
try:
npos_i = []
npos_i.append(np.array([75.0,95.0,15.0], dtype='float64'))
npos_i.append(np.array([-85.0,75.0,25.0], dtype='float64'))
npos_i.append(np.array([-96.0,-68.0,33.0], dtype='float64'))
npos_i.append(np.array([-85.0,-38.0,-78.0], dtype='float64'))
npos_j = []
npos_j.append(np.array([-101.0,-152.0,-45.0], dtype='float64'))
npos_j.append(np.array([-64.0,-32.0,131.0], dtype='float64'))
npos_j.append(np.array([-48.0,377.0,77.0], dtype='float64'))
npos_j.append(np.array([12.0,152.0,45.0], dtype='float64'))
npos_ij,nd_ij = pbc_i.delta_npos(npos_i,npos_j)
f = open('%s.test'%(tag), 'w')
for n in range(len(npos_i)):
pos_i = npos_i[n]
f.write(" pos_i %d [ %f %f %f ] \n"%(n+1,pos_i[0],pos_i[1],pos_i[2]))
for n in range(len(npos_j)):
pos_j = npos_j[n]
f.write(" pos_j %d [ %f %f %f ] \n"%(n+1,pos_j[0],pos_j[1],pos_j[2]))
for n in range(len(npos_i)):
for m in range(len(npos_j)):
pos_ij = npos_ij[n][m]
f.write(" pos_ij %d %d [ %f %f %f ] | %f | \n"%(n+1,m+1,pos_ij[0],pos_ij[1],pos_ij[2],nd_ij[n][m]))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.set_basis()'
tag='set_basis_2'
rshift=len(tag)+len(command)
try:
basis_i = pbc_i.return_basis()
f = open('%s.test'%(tag), 'w')
for n in range(3):
f.write(" Basis_o %d [ %f %f %f ] \n"%(n+1,basis_i[n,0],basis_i[n,1],basis_i[n,2]))
# Set local basis to new values
basis_i[0,0]=120.0
basis_i[1,1]=110.0
basis_i[2,2]=130.0
# Set lattice vectors to new values
pbc_i.set_basis(basis_i)
for n in range(3):
f.write(" Basis_i %d [ %f %f %f ] \n"%(n+1,basis_i[n,0],basis_i[n,1],basis_i[n,2]))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.delta_npos()'
tag='delta_npos_2'
rshift=len(tag)+len(command)
try:
basis_i = pbc_i.return_basis()
npos_i = []
npos_i.append(np.array([75.0,95.0,15.0], dtype='float64'))
npos_i.append(np.array([-85.0,75.0,25.0], dtype='float64'))
npos_i.append(np.array([-96.0,-68.0,33.0], dtype='float64'))
npos_i.append(np.array([-85.0,-38.0,-78.0], dtype='float64'))
npos_j = []
npos_j.append(np.array([-101.0,-152.0,-45.0], dtype='float64'))
npos_j.append(np.array([-64.0,-32.0,131.0], dtype='float64'))
npos_j.append(np.array([-48.0,377.0,77.0], dtype='float64'))
npos_j.append(np.array([12.0,152.0,45.0], dtype='float64'))
npos_ij,nd_ij = pbc_i.delta_npos(npos_i,npos_j)
f = open('%s.test'%(tag), 'w')
for n in range(3):
f.write(" Basis_o %d [ %f %f %f ] \n"%(n+1,basis_i[n,0],basis_i[n,1],basis_i[n,2]))
for n in range(len(npos_i)):
pos_i = npos_i[n]
f.write(" pos_i %d [ %f %f %f ] \n"%(n+1,pos_i[0],pos_i[1],pos_i[2]))
for n in range(len(npos_j)):
pos_j = npos_j[n]
f.write(" pos_j %d [ %f %f %f ] \n"%(n+1,pos_j[0],pos_j[1],pos_j[2]))
for n in range(len(npos_i)):
for m in range(len(npos_j)):
pos_ij = npos_ij[n][m]
f.write(" pos_ij %d %d [ %f %f %f ] | %f | \n"%(n+1,m+1,pos_ij[0],pos_ij[1],pos_ij[2],nd_ij[n][m]))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
command='pbc_i.delta_npos()'
tag='delta_npos_3'
rshift=len(tag)+len(command)
try:
basis_i = pbc_i.return_basis()
npos_i = []
npos_i.append(np.array([75.0,95.0,15.0], dtype='float64'))
npos_i.append(np.array([-85.0,75.0,25.0], dtype='float64'))
npos_i.append(np.array([-96.0,-68.0,33.0], dtype='float64'))
npos_i.append(np.array([-85.0,-38.0,-78.0], dtype='float64'))
npos_j = npos_i
npos_ij,nd_ij = pbc_i.delta_npos(npos_i,npos_j)
f = open('%s.test'%(tag), 'w')
for n in range(3):
f.write(" Basis_o %d [ %f %f %f ] \n"%(n+1,basis_i[n,0],basis_i[n,1],basis_i[n,2]))
for n in range(len(npos_i)):
pos_i = npos_i[n]
f.write(" pos_i %d [ %f %f %f ] \n"%(n+1,pos_i[0],pos_i[1],pos_i[2]))
for n in range(len(npos_j)):
pos_j = npos_j[n]
f.write(" pos_j %d [ %f %f %f ] \n"%(n+1,pos_j[0],pos_j[1],pos_j[2]))
for n in range(len(npos_i)):
for m in range(len(npos_j)):
pos_ij = npos_ij[n][m]
f.write(" pos_ij %d %d [ %f %f %f ] | %f | \n"%(n+1,m+1,pos_ij[0],pos_ij[1],pos_ij[2],nd_ij[n][m]))
f.close()
status='[PASSED]'.rjust(term_width-rshift)
except:
status='[FAILED]'.rjust(term_width-rshift)
if( os.system("diff %s.test %s.ref"%(tag,tag)) ):
status='[FAILED]'.rjust(term_width-rshift)
print "%s %s %s"%(tag,command,status)
test_list.append([tag,command,status.strip()])
tests_status = '[PASSED]'
for tag,command,status in test_list:
if ( status == '[FAILED]' ):
tests_status = '[FAILED]'
print "\n Testing of %s module %s"%(mod_name,tests_status)
update_ref = False
for tag,command,status in test_list:
os.system("cp %s.test %s.ref"%(tag,tag))
sys.exit(0)
def compute_pbc(filepath, bcoption='pbc', epsilons=[0.01], etas=[0.1]):
#pbc = PBC(bcoption=bcoption, is_get_bc_hyperedge=True)
pbc = PBC(bcoption=bcoption)
pbc.load_graph(filepath)
if bcoption == 'slpbc':
for eps in epsilons:
for eta in etas:
pbc.compute(eps=eps, eta=eta)
bc_path = get_bcpath(filepath, bcoption, eps=eps)
pbc.store_bc(bc_path)
if pbc.is_get_bc_hyperedge:
bc_path = get_bcpath(
filepath,
bcoption,
eps=eps,
is_get_bc_hyperedge=pbc.is_get_bc_hyperedge)
pbc.store_bcE(bc_path)
elif bcoption == 'naiveslpbc':
for eps in epsilons:
for eta in etas:
pbc.compute(eps=eps, eta=eta)
bc_path = get_bcpath(filepath, bcoption, eps=eps)
pbc.store_bc(bc_path)
if pbc.is_get_bc_hyperedge:
bc_path = get_bcpath(
filepath,
bcoption,
eps=eps,
is_get_bc_hyperedge=pbc.is_get_bc_hyperedge)
pbc.store_bcE(bc_path)
elif bcoption == 'bbc':
for eps in epsilons:
pbc.compute(eps=eps)
bc_path = get_bcpath(filepath, bcoption, eps=eps)
pbc.store_bc(bc_path)
else:
pbc.compute()
bc_path = get_bcpath(filepath, bcoption)
pbc.store_bc(bc_path)