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("--cif",
dest="writeCIF", action="store_true",
help="export cif files")
parser.add_option("--cif-dir",
dest="cifDir", default=".", action="store",type="string",
help="directory to write cifs to")
(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.writeCIF):
GMIN.initialize()
i=0
for m in db.minima():
i+=1
filename = options.cifDir+"/lowest%03d.cif"%(i)
print "minimum",i, "energy",m.energy,"to",filename
GMIN.writeCIF(filename, m.coords, "E"+str(m.energy))
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-disconnect",
dest="writeDPS", action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.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 args.writeDPS:
writeDPS(db)
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.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 args.write_pathsample:
write_pathsample_db(db)
parser.print_help()
exit(-1)
infile = args[0]
outfile = infile
# initialize GMIN
GMIN.initialize()
pot = gminpotential.GMINPotential(GMIN)
crystals.GMIN = GMIN
# open the storage class
db_in = Database(db=infile)
if(options.out!=None):
outfile = options.out
db_out = Database(db=outfile)
print("Start to reoptimize minima")
for m in db_in.minima():
print("optimizing minima",m._id,", energy", m.energy)
ret = dmagmin.quenchCrystal(m.coords, pot.getEnergyGradient, tol=options.tol, maxErise=options.maxErise)
print("new energy",ret[1],"(difference %f)"%(ret[1] - m.energy))
print()
if(options.out!=None):
db_out.addMinimum(ret[1], ret[0])
else:
m.energy = ret[1]
m.coords = ret[0]
db_in.session.commit()
import numpy as np
import oxdnagmin_ as GMIN
from pele.potentials.gminpotential import GMINPotential
import pele.basinhopping as bh
from pele.takestep import displace
from pele.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)
if len(args) != 1:
parser.print_help()
exit(-1)
infile = args[0]
outfile = infile
# initialize GMIN
GMIN.initialize()
pot = gminpotential.GMINPotential(GMIN)
crystals.GMIN = GMIN
# open the storage class
db_in = Database(db=infile)
if options.out != None:
outfile = options.out
db_out = Database(db=outfile)
print "Start to reoptimize minima"
for m in db_in.minima():
print "optimizing minima", m._id, ", energy", m.energy
ret = dmagmin.quenchCrystal(m.coords, pot.getEnergyGradient, tol=options.tol, maxErise=options.maxErise)
print "new energy", ret[1], "(difference %f)" % (ret[1] - m.energy)
print
if options.out != None:
db_out.addMinimum(ret[1], ret[0])
else:
m.energy = ret[1]
m.coords = ret[0]
db_in.session.commit()
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()
from builtins import range
import random
import pickle
from pele.storage.database import Database
#from math import pi
from pele.systems.oxdna import OXDNATakestep, export_xyz, OXDNAScrewStep
# number of trial configurations to try
nconf = 1000
# generate these from the n lowest minima
from_nlowest = 100
# open the database with minima
db = Database(db="storage.sqlite")
minima = db.minima()
# make sure from_nlowest is not larger than # of minima
from_nlowest = max(from_nlowest, len(minima))
# you can try a different step routine
step = OXDNATakestep(displace=0.0, rotate=0.8, rotate_around_backbone=False)
trial_configurations = []
for i in range(nconf):
x = random.choice(minima[0:nconf])
coords = x.coords.copy()
step.takeStep(coords)
trial_configurations.append(coords)
pickle.dump(trial_configurations, open("quench_benchmark.dat", "w"))
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():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("--write-dummy-db",
dest="write_pathsample_dummy", action="store_true",
help="generate a pathsample database without the points files - min.data and ts.data only")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("--minimum", type=int, default=0, help="print the coordinates of a particular minimum to the screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
parser.add_argument("-l",
dest="long_output", action="store_true",
help="Allow long output to be printed")
args = parser.parse_args()
if args.summary_long:
args.summary = True
suppress = not args.long_output
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db,suppress_long=suppress)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.minimum > 0:
m = db.getMinimum(args.minimum)
print m.energy, m._id
x = m.coords.reshape(-1,3)
print x
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.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 args.write_pathsample:
write_pathsample_db(db)
elif args.write_pathsample_dummy:
write_pathsample_db(db, False)
'''
Read structures from the database generated by the batch GA.
Run the run_batch.py script to generate a database.
@author: Mark Oakley
'''
import numpy as np
from pele.storage.database import Database
db = Database(db="mydatabase.sqlite")
minima=db.minima()
print(db.number_of_minima())
for i in minima:
print(i.energy)
print(np.reshape(i.coords,(-1,3)))
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)
