# PRINT INITIAL STRING I0 print "\nI0: ", print z #io.plotVector(prop[0][0],stringgraph,z, rangex=[-numpy.pi, numpy.pi], rangey=[-numpy.pi, numpy.pi]) dt = 1.0 for iter in range(0, numsteps): # NUMBER OF FTSM ITERATIONS for p in range(0, numpoints): # LOOPING OVER POINTS if (iter >= 10000 and iter <= 100000): kappa += (100. - 40.) / 90000. if (p != 0 or iter != 0): FTSM.setConstraint(PHI, PSI, phi=z[p][0], psi=z[p][1], kappa=kappa, forcefield=ff) # UPDATE FREE SPACE # USE FIRST SYSTEM TO GET M # USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES # FROM TARGETS zp0 = z[p][0] z[p][0] -= (kappa / gamma) * dt * (FTSM.M(x[p], PHI, PHI) * (z[p][0] - y[p].dihedral(PHI)) + FTSM.M(x[p], PHI, PSI) * (z[p][1] - y[p].dihedral(PSI))) z[p][1] -= (kappa / gamma) * dt * (FTSM.M(x[p], PSI, PHI) * (zp0 - y[p].dihedral(PHI)) + FTSM.M(x[p], PSI, PSI) *
'switching': 'C2' } ff.params['CoulombDiElec'] = { 'algorithm': 'Cutoff', 'switching': 'Cn', 'switchon': 10, 'cutoff': 12, 'order': 2 } for ii in range(0, numgridsquares): for jj in range(0, numgridsquares): print "BOX: ", ii, jj if (ii != 0): FTSM.setConstraint(PHI, PSI, midpts[ii][jj][0], midpts[ii][jj][1], kappa, ff) elif (jj != 0): FTSM.setConstraint(PHI, PSI, midpts[ii][jj][0], midpts[ii][jj][1], kappa, ff) pts = ii * numgridsquares + jj for i in range(0, 20): myProp.propagate(scheme="LangevinImpulse", steps=100, dt=1.0, forcefield=ff, params={ 'temp': 300, 'gamma': 91 })
#stringgraph=io.newGraph('Phi', 'Psi') # PRINT INITIAL STRING I0 print "\nI0: ", print z #io.plotVector(prop[0][0],stringgraph,z, rangex=[-numpy.pi, numpy.pi], rangey=[-numpy.pi, numpy.pi]) dt = 1.0 for iter in range(0, numsteps): # NUMBER OF FTSM ITERATIONS for p in range(0, numpoints): # LOOPING OVER POINTS if (iter >= 10000 and iter <= 100000): kappa += (100.-40.)/90000. if (p != 0 or iter != 0): FTSM.setConstraint(PHI, PSI, phi=z[p][0], psi=z[p][1], kappa=kappa, forcefield=ff) # UPDATE FREE SPACE # USE FIRST SYSTEM TO GET M # USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES # FROM TARGETS zp0 = z[p][0] z[p][0] -= (kappa/gamma)*dt*(FTSM.M(x[p], PHI, PHI)*(z[p][0]-y[p].dihedral(PHI)) + FTSM.M(x[p], PHI, PSI)*(z[p][1] - y[p].dihedral(PSI))) z[p][1] -= (kappa/gamma)*dt*(FTSM.M(x[p], PSI, PHI)*(zp0-y[p].dihedral(PHI)) + FTSM.M(x[p], PSI, PSI)*(z[p][1] - y[p].dihedral(PSI))) # UPDATE CARTESIAN prop[p][0].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300}) prop[p][1].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300})
'cutoff':12, 'switchon':10, 'switching':'C2'} ff.params['CoulombDiElec'] = {'algorithm':'Cutoff', 'switching':'Cn', 'switchon':10, 'cutoff':12, 'order':2} for ii in range(0,numgridsquares): for jj in range(0,numgridsquares): print "BOX: ", ii, jj if (ii !=0): FTSM.setConstraint(PHI, PSI, midpts[ii][jj][0],midpts[ii][jj][1],kappa,ff) elif (jj != 0) : FTSM.setConstraint(PHI, PSI, midpts[ii][jj][0],midpts[ii][jj][1],kappa,ff) pts = ii*numgridsquares + jj for i in range(0,20): myProp.propagate(scheme="LangevinImpulse",steps=100,dt=1.0,forcefield=ff,params={'temp':300,'gamma':91}) FTSM.setConstraint(PHI, PSI, midpts[ii][jj][0],midpts[ii][jj][1],kappa1,ff) #Equilibrate at this point for a bit myProp.propagate(scheme="LangevinImpulse",steps=50,dt=1.0,forcefield=ff,params={'temp':300,'gamma':91}) ef = outdir+'/sampleatrc.energies.'+str(ii)+'.'+str(jj) df = outdir+'/sampleatrc.'+str(ii)+'.'+str(jj)+'.dcd'