source: tests/Python/ForceAnnealing/pre/ising_model_chain.py@ 075357

import pyMoleCuilder as mol
import sys, os, math
try:
        import numpy
        numpy_present = True
except ImportError:
        numpy_present = False

if len(sys.argv) < 5:
        print 'Usage: '+sys.argv[0]+' <input> <path> <steps> <no_atoms> <use bondgraph>'
        sys.exit(1)

steps=int(sys.argv[3])
equilibrium_distance=1.6
no_atoms=int(sys.argv[4])
inputfile=sys.argv[1]
forcespath=sys.argv[2]
forcesfile="ising.forces"
use_bondgraph=sys.argv[5]

# creating input file
atomstart=7.6-1.6*math.floor(no_atoms/2)
print "Creating "+inputfile
with open(inputfile, 'w') as f:
        f.write("# ATOMDATA\ttype\tId\tx=3\tu=3\tF=3\tneighbors=4\n")
        f.write("# Box\t20\t0\t0\t0\t20\t0\t0\t0\t20\n")
        for i in range(1, no_atoms+1):
                atompos=atomstart+1.6*float(i)
                if i==math.floor(no_atoms/2+1):
                        atompos=atompos-.5
                if i==1:
                        f.write("C\t%d\t%lg\t10\t10\t0\t0\t0\t0\t0\t0\t%d\t0\t0\t0\n" % (i, atompos, i+1));
                elif i==no_atoms:
                        f.write("C\t%d\t%lg\t10\t10\t0\t0\t0\t0\t0\t0\t%d\t0\t0\t0\n" % (i, atompos, i-1));
                else:
                        f.write("C\t%d\t%lg\t10\t10\t0\t0\t0\t0\t0\t0\t%d\t%d\t0\t0\n" % (i, atompos, i-1, i+1));

print "Parsing from "+inputfile
mol.WorldInput(inputfile)
mol.SelectionAllAtoms()
mol.CommandVerbose("4")

# calculate damping factor from finite geometric series
# s_n/a = \sum^{n-1}_{k=0} r^k = (1-r^n)/(1-r) -> s_(n+1)/a -1 = \sum^{n}_{k=1} r^k = (1-r^(n+1))/(1-r) - 1
# \sum^{n}_{k=1} r^k := 1 and 1 = (1-r^(n+1))/(1-r) - 1 -> 2*(1-r) = 1 - r^(n+1) -> 1 - 2*r + r^(n+1) = 0
# find root: p[0] is coefficient of monomial with highest power 
if numpy_present:
        p=[0.] * (no_atoms+1)
        p[0]=1.
        p[no_atoms-1]=-2.
        p[no_atoms]=1.
        zeros=numpy.roots(p)
        print("Roots of p "+str(p)+" are "+str(zeros))
        damping=numpy.real(zeros[-1])
        print "Using damping factor of "+str(damping)
else:
        if no_atoms == 2:
                damping=0.5
        elif no_atoms == 5:
                damping=0.5436890126920764

for i in range(0, steps):
        # TODO: Python interface should have something to iterate over selected atoms
        # and molecules and get information on their internal status
        
        # read current atomic positions
        outputfile=forcespath+'/'+forcesfile+'.xyz'
        try:
                os.remove(outputfile)
        except: OSError
                #
        mol.WorldOutputAs(outputfile)
        mol.wait()
        distances=[]
        coords=[0.,0.,0.]
        try:
                skiplines=2+i*(1+1+no_atoms+1) # no_atoms, comment, no_atoms atoms, empty line
                with open(outputfile) as f:
                        for line in f:
                                if skiplines != 0:
                                        skiplines=skiplines-1
                                        continue
                                line=line.replace('\t',' ')
                                print "LINE: "+line
                                [elementtype, X, Y, Z] = line.split(' ', 4)
                                if coords!=[0.,0.,0.]:
                                        distances.append(math.sqrt((coords[0]-float(X))**2+(coords[1]-float(Y))**2+(coords[2]-float(Z))**2))
                                coords=[float(X),float(Y),float(Z)]
        except IOError:
                print 'Warning: '+outputfile+' not readable.'
                sys.exit(1)
        
        assert(len(distances)==no_atoms-1)
        
        # 
        # generate Ising model forces and store in file
        #
        # i.e. we have spring forces between neighboring atoms depending on their distance
        forces=[]
        for d in distances:
                forces.append( d - equilibrium_distance );
                
        # generate new forces file
        
        with open(forcespath+'/'+forcesfile, 'w') as f:
                f.write('# atom\tf_x\tf_y\tf_z\n')
                for i in range(len(distances)+1):
                        force=0
                        if i!=0:
                                force=force-forces[i-1]
                        if (i != len(distances)):
                                force=force+forces[i]
                        f.write("%d\t%f\t0.\t0.\n" % (i+1, force))

        mol.WorldStepWorldTime("1")
        mol.MoleculeForceAnnealing(forcespath+'/'+forcesfile, ".1", "%d" % (steps), "%d" % (no_atoms-1), "%lg" % (damping), use_bondgraph)
        mol.wait()
        
sys.exit(0)