def test():
from pygmin.systems import LJCluster
natoms = 13
system = LJCluster(natoms)
db = system.create_database()
# get some minima
bh = system.get_basinhopping(database=db, outstream=None)
bh.run(100)
manager = ConnectManager(db, clust_min=2)
for i in range(4):
min1, min2 = manager.get_connect_job(strategy="random")
print "connecting", min1._id, min2._id
connect = system.get_double_ended_connect(min1, min2, db, verbosity=0)
connect.connect()
print "\n\ntesting untrap"
for i in range(10):
min1, min2 = manager.get_connect_job(strategy="untrap")
print min1._id, min2._id
print "\n\ntesting combine"
for i in range(5):
min1, min2 = manager.get_connect_job(strategy="combine")
print min1._id, min2._id
print "\n\ntesting gmin"
for i in range(5):
min1, min2 = manager.get_connect_job(strategy="gmin")
print min1._id, min2._id
def test():
from pygmin.systems import LJCluster
natoms = 13
system = LJCluster(natoms)
db = system.create_database()
# get some minima
bh = system.get_basinhopping(database=db, outstream=None)
bh.run(100)
manager = ConnectManager(db, clust_min=2)
for i in range(4):
min1, min2 = manager.get_connect_job(strategy="random")
print "connecting", min1._id, min2._id
connect = system.get_double_ended_connect(min1, min2, db, verbosity=0)
connect.connect()
print "\n\ntesting untrap"
for i in range(10):
min1, min2 = manager.get_connect_job(strategy="untrap")
print min1._id, min2._id
print "\n\ntesting combine"
for i in range(5):
min1, min2 = manager.get_connect_job(strategy="combine")
print min1._id, min2._id
print "\n\ntesting gmin"
for i in range(5):
min1, min2 = manager.get_connect_job(strategy="gmin")
print min1._id, min2._id
def spawnlj(**kwargs):
from pygmin.systems import LJCluster
from pygmin.config import config
import os
natoms = 13
sys = LJCluster(natoms)
db = sys.create_database()
x1, E1 = sys.get_random_minimized_configuration()[:2]
x2, E2 = sys.get_random_minimized_configuration()[:2]
m1 = db.addMinimum(E1, x1)
m2 = db.addMinimum(E2, x2)
optim = "/home/js850/git/OPTIM/source/build/OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
spawner = SpawnOPTIM_LJ(x1, x2, sys, OPTIM=optim, **kwargs)
spawner.run()
spawner.load_results(db)
def spawnlj(**kwargs):
from pygmin.systems import LJCluster
from pygmin.config import config
import os
natoms = 13
sys = LJCluster(natoms)
db = sys.create_database()
x1, E1 = sys.get_random_minimized_configuration()[:2]
x2, E2 = sys.get_random_minimized_configuration()[:2]
m1 = db.addMinimum(E1, x1)
m2 = db.addMinimum(E2, x2)
optim = "/home/js850/git/OPTIM/source/build/OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
spawner = SpawnOPTIM_LJ(x1, x2, sys, OPTIM=optim, **kwargs)
spawner.run()
spawner.load_results(db)
def get_database(natoms=13, nconn=5):
"""create a database for a lennard jones system
fill it with minima from a basinhopping run, then connect
some of those minima using DoubleEndedConnect
"""
ljsys = LJCluster(natoms)
db = ljsys.create_database()
bh = ljsys.get_basinhopping(database=db, outstream=None)
while (len(db.minima()) < nconn + 1):
bh.run(100)
minima = list(db.minima())
m1 = minima[0]
for m2 in minima[1:nconn + 1]:
connect = ljsys.get_double_ended_connect(m1, m2, db)
connect.connect()
return db
def get_database(natoms=13, nconn=5):
"""create a database for a lennard jones system
fill it with minima from a basinhopping run, then connect
some of those minima using DoubleEndedConnect
"""
ljsys = LJCluster(natoms)
db = ljsys.create_database()
bh = ljsys.get_basinhopping(database=db, outstream=None)
while len(db.minima()) < nconn + 1:
bh.run(100)
minima = list(db.minima())
m1 = minima[0]
for m2 in minima[1 : nconn + 1]:
connect = ljsys.get_double_ended_connect(m1, m2, db)
connect.connect()
return db
self.nsteps = nsteps
self.mcstep = RandomDisplacement(stepsize=stepsize)
def takeStep(self, coords, **kwargs):
#make a new monte carlo class
mc = MonteCarlo(coords, self.potential, self.mcstep,
temperature = self.T, outstream=None)
mc.run( self.nsteps )
coords[:] = mc.coords[:]
def updateStep(self, acc, **kwargs):
pass
natoms = 12
niter = 100
system = LJCluster(natoms)
db = system.create_database()
# create takestep routine manually
potential = system.get_potential()
step = TakeStepMonteCarlo(potential)
bh = system.get_basinhopping(database=db, takestep=step)
bh.run(niter)
print "the lowest energy found after", niter, " basinhopping steps is", db.minima()[0].energy
print ""
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster
pl.ion()
natoms = 13
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms,)
db = system.create_database(dbname)
#get some minima
if False:
bh = system.get_basinhopping(database=db)
bh.run(10)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
# connect some of the minima
"""
Example 2: reading coords from file
"""
import numpy as np
from pygmin.systems import LJCluster
natoms = 12
niter = 100
system = LJCluster(natoms)
coords = np.loadtxt('coords')
coords = coords.reshape(-1)
db = system.create_database()
bh = system.get_basinhopping(database=db)
bh.run(niter)
print "the lowest energy found after", niter, " basinhopping steps is", db.minima()[0].energy
print ""
from random import choice
from pygmin.systems import LJCluster
from pygmin.storage import Minimum
from pygmin.concurrent import RandomConnectServer
server_name = "ljconnect_example"
hostname="localhost"
port=11567
print "setting up LJ38 with database lj38.sqlite"
system = LJCluster(38)
db = system.create_database("lj38.sqlite")
if db.session.query(Minimum).count() < 10:
print "The database is empty, run basinhopping to get some minima"
bh = system.get_basinhopping(database=db)
bh.run(100)
print "Working on %d minima"%db.session.query(Minimum).count()
print "Running basinhopping to generate initial database"
print "Creating new connect manager"
connect_manager=RandomConnectServer(system, db, server_name=server_name,
host=hostname, port=port)
connect_manager.run()
Since we don't already have a database, for this example we'll build a small one using
basinhopping"
"""
import numpy as np
import logging
from pygmin.systems import LJCluster
from pygmin.utils.disconnectivity_graph import DisconnectivityGraph, database2graph
natoms = 13
system = LJCluster(natoms)
use_existing_database = False
if use_existing_database:
db = system.create_database("lj13.sqlite", createdb=False)
else:
# build a small database using basinhopping
print "building a small database using basinhopping" ""
db = system.create_database()
bh = system.get_basinhopping(database=db, outstream=None)
bh.run(20)
print "starting with a database of", len(db.minima()), "minima"
# turn of status printing for the connect run
# first use the logging module to turn off the status messages
logger = logging.getLogger("pygmin.connect")
logger.setLevel("WARNING")
else:
faccept = float(ndiff_accept) / ndiff
if faccept > self.target_new_min_accept_prob:
driver.acceptTest.temperature *= self.Tfactor
else:
driver.acceptTest.temperature /= self.Tfactor
if self.verbose:
print " temperature is now %.4g ratio %.4g target %.4g" % (driver.acceptTest.temperature,
faccept, self.target_new_min_accept_prob)
if __name__ == "__main__":
import numpy as np
from pygmin.takestep import displace
from pygmin.systems import LJCluster
#from pygmin.takestep import adaptive
natoms = 38
sys = LJCluster(natoms=38)
# random initial coordinates
coords = sys.get_random_configuration()
takeStep = displace.RandomDisplacement( stepsize=0.4 )
tsAdaptive = AdaptiveStepsizeTemperature(takeStep, interval=300, verbose=True)
db = sys.create_database()
opt = sys.get_basinhopping(database=db, takestep=tsAdaptive, coords=coords)
opt.printfrq = 50
opt.run(5000)
else:
faccept = float(ndiff_accept) / ndiff
if faccept > self.target_new_min_accept_prob:
driver.acceptTest.temperature *= self.Tfactor
else:
driver.acceptTest.temperature /= self.Tfactor
if self.verbose:
print " temperature is now %.4g ratio %.4g target %.4g" % (driver.acceptTest.temperature,
faccept, self.target_new_min_accept_prob)
if __name__ == "__main__":
import numpy as np
from pygmin.takestep import displace
from pygmin.systems import LJCluster
#from pygmin.takestep import adaptive
natoms = 38
sys = LJCluster(natoms=38)
# random initial coordinates
coords = sys.get_random_configuration()
takeStep = displace.RandomDisplacement( stepsize=0.4 )
tsAdaptive = AdaptiveStepsizeTemperature(takeStep, interval=300, verbose=True)
db = sys.create_database()
opt = sys.get_basinhopping(database=db, takestep=tsAdaptive, coords=coords)
opt.printfrq = 50
opt.run(5000)
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster
pl.ion()
natoms = 13
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms, )
db = system.create_database(dbname)
#get some minima
if False:
bh = system.get_basinhopping(database=db)
bh.run(10)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
# connect some of the minima
nmax = min(3, len(minima))
self.ui.label.setText(label)
if with_path:
coordspath = np.array(self.quench_path)
self.ui.show3d.setCoordsPath(coordspath, frame=-1)
else:
self.ui.show3d.setCoords(self.coords, index=2)
self.ui.show3d.setCoords(self.quenched, index=1)
if __name__ == "__main__":
import sys
import pylab as pl
from OpenGL.GLUT import glutInit
glutInit()
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster
pl.ion()
natoms = 13
system = LJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
db = system.create_database(db=":memory:")
system.database = db
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
wnd = TakestepExplorer(app=app, system=system, database = db)
wnd.show()
from PyQt4.QtCore import QTimer
sys.exit(app.exec_())
