def eval_bond_coul(self, occm_trial, nneocc_trial):
logger.debug("charging effects are active")
occm_ch, ntot_ch = SupportFunctions.identify(self.args.n, self.args.m, occm_trial, nneocc_trial, self.args.n_thresh_ch)
nneocc_scr_trial = SupportFunctions.occneigh2(self.args.n, self.args.m, occm_ch, occm_trial, self.icind)
ictot_scr_trial = SupportFunctions.totnoneigh2(self.args.n, self.args.m, nneocc_scr_trial, False)
logger.debug('evaluating neights based off of coloumbic interaction')
escreen = -self.args.beta_scr * (ictot_scr_trial - ntot_ch * self.args.n_thresh_ch)
logger.debug("screnmol, energy: {0} {1} {2} ".format(ntot_ch, ictot_scr_trial, escreen))
logger.debug("now determines charged 1st nn's")
nneocc_ch_trial = SupportFunctions.occneigh2(self.args.n, self.args.m, occm_ch, occm_ch, self.icind)
logger.debug('computing number of charge bonds and such coulombic energy')
ictot_ch_trial = SupportFunctions.totnoneigh2(self.args.n, self.args.m, nneocc_ch_trial, True)
ecoulrep = self.args.beta_coul * ictot_ch_trial
return ecoulrep, escreen, occm_ch, nneocc_ch_trial, ntot_ch, ictot_ch_trial
def eval_bond_coul2nd(self, occm_ch, nneocc_ch_trial):
logger.debug("now determining charged 2nd neighbour's")
sec_nneocc_ch_trial = SupportFunctions.sec_neigh(self.args.n, self.args.m, occm_ch, nneocc_ch_trial, self.icind)
icsec_ch_trial = SupportFunctions.totnoneigh2(self.args.n, self.args.m, sec_nneocc_ch_trial, True)
ecoulrep_sec = self.args.beta_sec_coul * icsec_ch_trial
logger.debug("2nd neighbour coloumbic energy: {0}".format(ecoulrep_sec))
return ecoulrep_sec
def setup(self):
if self.args.brestart:
self.occm = numpy.zeros([self.args.n * self.args.m], dtype=numpy.bool)
ifile = open(self.args.inp_filenm, 'r')
self.etot = 0.0
self.args.n = numpy.load(ifile)
self.args.m = numpy.load(ifile)
self.ntotmol = numpy.load(ifile)
self.occm = numpy.load(ifile)
self.etot = numpy.load(ifile)
ifile.close()
# a dictionary to store energy values in
# determines all positions and indices vectors
self.allpos, self.allind, self.ic, self.pos = SupportFunctions.allpositions(self.args.n, self.args.m, self.args.b)
#determines the index file of all neighbours
self.allneigh = numpy.zeros([self.args.n*self.args.m, 6, 2], dtype=numpy.int)
self.icind = numpy.zeros([self.args.n*self.args.m, 6], dtype=numpy.int)
self.allneigh, self.icind = SupportFunctions.allneighbors(self.allind, self.ic, self.args.n, self.args.m)
if not self.args.brestart:
self.occm, self.ntotmol = SupportFunctions.randdistr(self.args.n, self.args.m, self.args.cov)
#colours the molecules (occupied sites)
#determines their neighbours
self.nneocc = SupportFunctions.occneigh(self.args.n, self.args.m, self.occm, self.icind)
# counts the bonds (shared edges)
self.ictot = SupportFunctions.totnoneigh2(self.args.n, self.args.m, self.nneocc, True)
# total energy
self.evdW = -1.0*self.args.beta*self.ictot
# total energy for the moment just vdW
if not self.args.brestart:
self.etot = self.evdW
#
logger.info('Temperature: {0}'.format(self.args.kt))
logger.info('INITIAL energy/mol: {0}'.format(self.etot/float(self.ntotmol)))
# makes a little metropolis animation
self.entropy = 0.0
self.escreen = 0.0
self.ecoulrep = 0.0
self.ecoulrep_sec = 0.0
self.jfrom = 0
self.jto = 0
self.icmov = 0
self.cluster_type = 0
def eval_bond_vdw(self, occm_trial):
nneocc_trial = SupportFunctions.occneigh(self.args.n, self.args.m, occm_trial, self.icind)
ictot_trial = SupportFunctions.totnoneigh2(self.args.n, self.args.m, nneocc_trial, True)
evdW_trial = -self.args.beta * ictot_trial
return evdW_trial, ictot_trial, nneocc_trial
