Esempio n. 1
0
    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
Esempio n. 2
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