+ w0[n]
),
)
return np.array(ww)
else:
print("We can't indentify the mode")
sys.exit()
# -----END of some functions-----------------
# -----READ---------------------------------
print("\nWe are ready to start. Reading {} ... (This can take a while)".format(inputt))
simulation = Simulation.load_from_xml(
inputt, custom_verbosity="quiet", request_banner=False, read_only=True
)
# xmlrestart = xml_parse_file(open(inputt))
# input_simulation = isimulation.InputSimulation()
# input_simulation.parse(xmlrestart.fields[0][1])
# simulation = input_simulation.fetch()
# simulation.bind(read_only=True)
beads = simulation.syslist[0].motion.beads.copy()
m = simulation.syslist[0].motion.beads.m.copy()
nbeads = simulation.syslist[0].motion.beads.nbeads
natoms = simulation.syslist[0].motion.beads.natoms
if case == "reactant":
if nbeadsR == 0:
ret = read_file("xyz", ipos)
pos.append(ret["atoms"])
cell = ret["cell"]
nbeads += 1
except EOFError: # finished reading files
break
ipos.close()
natoms = pos[0].natoms
atom = pos[0]
# Compose the half ring polymer.
q = np.vstack([i.q for i in pos])
else:
from ipi.engine.simulation import Simulation
if (os.path.exists(chk)):
simulation = Simulation.load_from_xml(chk, custom_verbosity='low', request_banner=False)
else:
print "We can't find %s " % chk
sys.exit()
cell = simulation.syslist[0].cell
beads = simulation.syslist[0].motion.beads.copy()
natoms = simulation.syslist[0].motion.beads.natoms
nbeads = beads.nbeads
q = beads.q
atom = beads._blist[0]
print ' '
print 'We have a half ring polymer made of %i beads and %i atoms.' % (nbeads, natoms)
print 'We will expand the ring polymer to get a half polymer of %i beads.' % nbeadsNew
# Compose the full ring polymer.
return np.array(ww)
else:
print "We can't indentify the mode"
sys.exit()
#-----END of some functions-----------------
#-----READ---------------------------------
print ''
print 'We are ready to start'
print 'Reading %s ...' % inputt
print '(This can take a while)'
simulation = Simulation.load_from_xml(inputt,
custom_verbosity='low',
request_banner=False)
beads = simulation.syslist[0].motion.beads.copy()
m = simulation.syslist[0].motion.beads.m.copy()
nbeads = simulation.syslist[0].motion.beads.nbeads
natoms = simulation.syslist[0].motion.beads.natoms
if case == 'reactant':
if nbeadsR == 0:
print 'We have to specify number of beads for computing the partition function in the reactant case'
sys.exit()
if case != 'instanton' and nbeads > 1:
print 'Incompatibility between case and nbeads in %s.' % (inputt)
print 'case %s' % case
print 'beads %i' % nbeads
cell = ret["cell"]
nbeads += 1
except EOFError: # finished reading files
break
ipos.close()
natoms = pos[0].natoms
atom = pos[0]
# Compose the half ring polymer.
q = np.vstack([i.q for i in pos])
else:
from ipi.engine.simulation import Simulation
if os.path.exists(chk):
simulation = Simulation.load_from_xml(
chk, custom_verbosity="low", request_banner=False, read_only=True
)
else:
print("We can't find {}".format(chk))
sys.exit()
cell = simulation.syslist[0].cell
beads = simulation.syslist[0].motion.beads.copy()
natoms = simulation.syslist[0].motion.beads.natoms
nbeads = beads.nbeads
q = beads.q
atom = beads._blist[0]
print(" ")
print(
"We have a half ring polymer made of {} beads and {} atoms.".format(
nbeads, natoms