import oxdnagmin_ as GMIN from pygmin.potentials.gminpotential import GMINPotential import pygmin.basinhopping as bh from pygmin.takestep import displace from pygmin.storage.database import Database # initialize GMIN GMIN.initialize() # create a potential which calls GMIN potential = GMINPotential(GMIN) # get the initial coorinates coords = potential.getCoords() coords = np.random.random(coords.shape) # create takestep routine step = displace.RandomDisplacement(stepsize=1.) # store all minima in a database db = Database(db="storage.sqlite", accuracy=1e-2) # create Basinhopping object opt = bh.BasinHopping(coords, potential, step, db.minimum_adder()) # run for 100 steps opt.run(1000) # now dump all the minima i = 0 for m in db.minima(): i += 1 GMIN.userpot_dump("lowest_%03d.dat" % (i), m.coords)
coords=potential.getCoords() coords=np.random.random(coords.shape) # create takestep routine # we combine a normal step taking group = takestep.BlockMoves() step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace, rotate=0.), frequency=50) step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0., rotate=parameters.rotate), frequency=50) group.addBlock(100, step1) group.addBlock(100, step2) # with a generate random configuration genrandom = OXDNAReseed() # in a reseeding takestep procedure reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed) # store all minima in a database db = Database(db="storage.sqlite", accuracy=1e-2) # create Basinhopping object opt = BasinHopping(coords, potential, reseed, db.minimum_adder(), temperature=parameters.temperature) # run for 100 steps opt.run(parameters.nsteps) # now dump all the minima i=0 for m in db.minima(): i+=1 GMIN.userpot_dump("lowest_%03d.dat"%(i), m.coords)
def main(): # add some program options parser = OptionParser(usage="usage: %prog [options] storage") parser.add_option( "--write-disconnect", dest="writeDPS", action="store_true", help="generate min.dat and ts.dat to use with disconnectDPS") parser.add_option("-m", dest="writeMinima", action="store_true", help="dump minima to screen") parser.add_option("-t", dest="writeTS", action="store_true", help="dump transition states to screen") parser.add_option("--coords", dest="writeCoords", action="store_true", help="export coordinates files") parser.add_option("--xyz", dest="writeXYZ", action="store_true", help="export xyz files") (options, args) = parser.parse_args() # print help if no input file is given if (len(args) != 1): parser.print_help() exit(-1) db = Database(db=args[0]) if (options.writeMinima): print "List of minima:" print "---------------" for m in db.minima(): print "%f\t\tid %d" % (m.energy, m._id) print "END\n" if (options.writeTS): print "List of transition states:" print "--------------------------" for ts in db.transition_states(): print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\ (ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy) print "END\n" if (options.writeDPS): writeDPS(db) if (options.writeCoords): GMIN.initialize() i = 0 for m in db.minima(): i += 1 filename = "lowest/lowest%03d.cif" % (i) print "minimum", i, "energy", m.energy, "to", filename GMIN.userpot_dump(filename, m.coords) if (not TO_PDB is None): os.system(TO_PDB % filename) np.savetxt("lowest/coords_%03d.txt" % (i), m.coords) if (options.writeXYZ): traj = open("lowest/traj.xyz", "w") i = 0 for m in db.minima(): i += 1 filename = "lowest/lowest%03d.xyz" % (i) print "minimum", i, "energy", m.energy, "to", filename export_xyz(open(filename, "w"), m.coords) export_xyz(traj, m.coords) traj.close()
def main(): # add some program options parser = OptionParser(usage = "usage: %prog [options] storage") parser.add_option("--write-disconnect", dest="writeDPS", action="store_true", help="generate min.dat and ts.dat to use with disconnectDPS") parser.add_option("-m", dest="writeMinima", action="store_true", help="dump minima to screen") parser.add_option("-t", dest="writeTS", action="store_true", help="dump transition states to screen") parser.add_option("--coords", dest="writeCoords", action="store_true", help="export coordinates files") parser.add_option("--xyz", dest="writeXYZ", action="store_true", help="export xyz files") (options, args) = parser.parse_args() # print help if no input file is given if(len(args) != 1): parser.print_help() exit(-1) db = Database(db=args[0]) if(options.writeMinima): print "List of minima:" print "---------------" for m in db.minima(): print "%f\t\tid %d"%(m.energy, m._id) print "END\n" if(options.writeTS): print "List of transition states:" print "--------------------------" for ts in db.transition_states(): print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\ (ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy) print "END\n" if(options.writeDPS): writeDPS(db) if(options.writeCoords): GMIN.initialize() i=0 for m in db.minima(): i+=1 filename = "lowest/lowest%03d.cif"%(i) print "minimum",i, "energy",m.energy,"to",filename GMIN.userpot_dump(filename, m.coords) if(not TO_PDB is None): os.system(TO_PDB%filename) np.savetxt("lowest/coords_%03d.txt"%(i), m.coords) if(options.writeXYZ): traj=open("lowest/traj.xyz", "w") i=0 for m in db.minima(): i+=1 filename = "lowest/lowest%03d.xyz"%(i) print "minimum",i, "energy",m.energy,"to",filename export_xyz(open(filename, "w"), m.coords) export_xyz(traj, m.coords) traj.close()