# translational eigenvectors
x1 = np.zeros(coords.shape)
x2 = x1.copy()
x3 = x1.copy()
x1.reshape(coords.size/3,3)[0:2,0] = 1.
x2.reshape(coords.size/3,3)[0:2,1] = 1.
x3.reshape(coords.size/3,3)[0:2,2] = 1.
return [x1/np.linalg.norm(x1), x2/np.linalg.norm(x2), x3/np.linalg.norm(x3)]
def findTS(self, coords):
from pygmin.optimize import fire
pot = gminpot.GMINPotential(GMIN)
tau = np.random.random(coords.shape) - 0.5
tau[-6:]=0.
from pygmin import defaults
import pygmin.optimize.transition_state.transition_state_refinement as tsr
defaults.quenchParams["maxstep"]=0.01
defaults.quenchParams["tol"]=1.e-4
defaults.quenchRoutine = fire
ret = dimer.findTransitionState(coords+1e-2*tau, pot, direction=tau, zeroEigenVecs=self.zeroEigenVecs, tol=1e-4, maxstep=0.01)
#ret = tsr.findTransitionState(coords+1e-2*tau, pot, tol=1e-4)
print "TS:",ret.energy
m1,m2 = tstools.minima_from_ts(pot.getEnergyGradient, ret.coords, ret.eigenvec, displace=1e-1)
print "Energies: ", m1[1],ret.energy,m2[1]
return [ret.coords,ret.energy],m1,m2
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(CrystalSystem)
def run_gui(system, db=None):
import pygmin.gui.run as gr
gr.run_gui(system, db=db)
def run_gui(system):
import pygmin.gui.run as gr
gr.run_gui(system)
super(LJSystem, self).__init__(self.natoms)
self.params.gui.basinhopping_nsteps = 1000
def get_optim_spawner(self, coords1, coords2):
from pygmin.systems.spawn_OPTIM import SpawnOPTIM_LJ
import os
# # TODO: this should be passable somehow
# optim = os.path.expanduser("~")+"/git/OPTIM/source/build/OPTIM"
## optim = "OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
print "optim executable", optim
return SpawnOPTIM_LJ(coords1, coords2, self, OPTIM=optim, tempdir=True)
class NewLJDialog(QtGui.QDialog, NewLJ.Ui_DialogLJSetup):
def __init__(self):
QtGui.QDialog.__init__(self)
self.setupUi(self)
def natoms(self):
return int(self.lineNatoms.text())
def nsave(self):
return int(self.lineNsave.text())
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(LJSystem)
from PyQt4 import QtGui
from ljsystem import NewLJDialog
from pygmin.systems import BLJCluster
class BLJSystem(BLJCluster):
def __init__(self):
dlg = NewLJDialog()
dlg.exec_()
self.natoms = dlg.natoms()
super(BLJSystem, self).__init__(self.natoms)
if dlg.result() == QtGui.QDialog.Rejected:
raise BaseException("Aborted parameter dialog")
def findTS(self, coords):
raise NotImplementedError
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(BLJSystem)
def run_gui(system):
import pygmin.gui.run as gr
gr.run_gui(system)
from PyQt4 import QtGui
from ljsystem import NewLJDialog
from pygmin.systems import BLJCluster
class BLJSystem(BLJCluster):
def __init__(self):
dlg = NewLJDialog()
dlg.exec_()
self.natoms = dlg.natoms()
super(BLJSystem, self).__init__(self.natoms)
if dlg.result() == QtGui.QDialog.Rejected:
raise BaseException("Aborted parameter dialog")
def findTS(self, coords):
raise NotImplementedError
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(BLJSystem)
def rungui(system, db=None):
import pygmin.gui.run as gr
from pygmin.storage import Database
gr.run_gui(system, db=db)
import gmin_ as GMIN
from pygmin.potentials import GMINPotential
from pygmin.systems import LJCluster
import numpy as np
class GUPTASystem(LJCluster):
def __init__(self):
GMIN.initialize()
self.natoms = GMIN.getNAtoms()
super(GUPTASystem, self).__init__(self.natoms)
qp = self.params.structural_quench_params
qp["tol"]=1e-5
qp["maxErise"]=1e-5
qp["maxstep"]=0.1
qp["iprint"]=-1
qp["debug"]=False
neb = self.params.double_ended_connect.local_connect_params.NEBparams
neb["image_density"]=5
neb["adjustk_freq"]=5
def get_potential(self):
return GMINPotential(GMIN)
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(GUPTASystem)
def draw(self, coordsl, index):
from OpenGL import GL,GLUT
coords=coordsl.reshape(coordsl.size/3,3)
#coords = coords.reshape(GMIN.getNAtoms, 3)
com=np.mean(coords, axis=0)
for xx in coords:
x = xx-com
GL.glPushMatrix()
GL.glTranslate(x[0],x[1],x[2])
GLUT.glutSolidSphere(0.3,30,30)
GL.glPopMatrix()
# get bond list from amber params
mol = readAmb.readAmberParam()
mol.populateBondConn()
# draw bonds
for atomPairs in mol.bondConn:
xyz1 = coords[atomPairs[0]-1] - com
xyz2 = coords[atomPairs[1]-1] - com
self.drawCylinder(xyz1, xyz2)
def createNEB(self, coords1, coords2):
pot = gminpot.GMINPotental(GMIN)
return NEB.NEB(coords1, coords2, pot, k = 100. ,nimages=20)
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(molSystem)
ca1 = CoordsAdapter(nrigid=coords1.size/6, coords = coords1)
ca2 = CoordsAdapter(nrigid=coords2.size/6, coords = coords2)
rot = rmsfit.findrotation_kabsch(ca2.posRigid, ca1.posRigid)
ca2.posRigid[:] = np.dot(rot,ca2.posRigid.transpose()).transpose()
for p in ca2.rotRigid:
p[:] = rotations.mx2aa((np.dot(rot, rotations.aa2mx(p))))
print "before"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
for p1,p2 in zip(ca1.rotRigid, ca2.rotRigid):
p1[:],p2[:] = aamindist.aadistance(p1, p2)
print "after"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
path = InterpolatedPath(coords1, coords2, 40)
print potential.getEnergy(path[0])
print "Interpolated energies"
for x in InterpolatedPath(coords1, coords2, 40):
print potential.getEnergy(x)
print "done"
return coords1, coords2
def createNEB(self, coords1, coords2):
return NEB(InterpolatedPath(coords1, coords2, 40), GMINPotential(GMIN), k = 100.)
if __name__ == "__main__":
GMIN.initialize()
gr.run_gui(OXDNASystem)
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def get_compare_exact(self, **kwargs):
return ExactMatchAACluster(self.aasystem,
accuracy=0.1,
tol=0.07,
**kwargs)
def get_mindist(self, **kwargs):
return MinPermDistAACluster(self.aasystem,
accuracy=0.1,
tol=0.07,
**kwargs)
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(PAPSystem, db="pap.sqlite")
water = create_pap()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
return system
def get_compare_exact(self, **kwargs):
return ExactMatchAACluster(self.aasystem, accuracy=0.1, tol=0.07, **kwargs)
def get_mindist(self, **kwargs):
return MinPermDistAACluster(self.aasystem,accuracy=0.1, tol=0.07, **kwargs)
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(PAPSystem, db="pap.sqlite")
def rungui(system, db=None):
import pygmin.gui.run as gr
from pygmin.storage import Database
gr.run_gui(system, db=db)
def draw(self, coordsl, index):
from OpenGL import GL, GLUT
coords = coordsl.reshape(coordsl.size / 3, 3)
#coords = coords.reshape(GMIN.getNAtoms, 3)
com = np.mean(coords, axis=0)
for xx in coords:
x = xx - com
GL.glPushMatrix()
GL.glTranslate(x[0], x[1], x[2])
GLUT.glutSolidSphere(0.3, 30, 30)
GL.glPopMatrix()
# get bond list from amber params
mol = readAmb.readAmberParam()
mol.populateBondConn()
# draw bonds
for atomPairs in mol.bondConn:
xyz1 = coords[atomPairs[0] - 1] - com
xyz2 = coords[atomPairs[1] - 1] - com
self.drawCylinder(xyz1, xyz2)
def createNEB(self, coords1, coords2):
pot = gminpot.GMINPotental(GMIN)
return NEB.NEB(coords1, coords2, pot, k=100., nimages=20)
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(molSystem)
from pygmin.amber import amberSystem
# create new amber system
sys = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
#start the gui
from pygmin.gui import run as gr
gr.run_gui(sys)
GL.glTranslate( X1[0], X1[1], X1[2] )
GL.glRotate( a, t[0], t[1], t[2] )
GLUT.glutSolidCone(.2,r,30,30) #I can't seem to draw a cylinder
GL.glPopMatrix()
def Align(self, coords1, coords2):
from pygmin.mindist.minpermdist_rbmol import minPermDistRBMol as minpermdist
dist, X1, X2 = minpermdist( coords1, coords2, self.mysys, niter = 100 )
return X1, X2
def createNEB(self, coords1, coords2):
return NEB.NEB(coords1, coords2, self.mysys, k = 100., nimages=20)
class NewLJDialog(QtGui.QDialog,NewLJ.Ui_DialogLJSetup):
def __init__(self):
QtGui.QDialog.__init__(self)
self.setupUi(self)
def natoms(self):
return int(self.lineNatoms.text())
def nsave(self):
return int(self.lineNsave.text())
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(RBSystem)
#print 'GMIN POTENTIAL'
#sys = AMBERSystem_GMIN('coords.prmtop', 'coords.inpcrd')
#sys.test_potential('coords.pdb')
# openmm potential is ~6x slower than gmin potential
print 'OPENmm POTENTIAL'
sys = AMBERSystem_OpenMM('coords.prmtop', 'coords.inpcrd')
sys.test_potential('coords.pdb')
# create new database
from pygmin.storage import Database
dbcurr = sys.create_database()
# ------- TEST gui
from pygmin.gui import run as gr
gr.run_gui(sys, db=dbcurr)
# ------ Test potential
sys.test_potential('coords.pdb')
# ------ BH
start = time.clock()
sys.test_BH(dbcurr)
elapsed = (time.clock() - start)
print "time taken by BH = ", elapsed
exit()
# ------- Connect runs
sys.test_connect(dbcurr)
# ------- Disconn graph
# create new amber system
sysAmb = AMBERSystem('/home/ss2029/WORK/PyGMIN/examples/amber/coords.prmtop', '/home/ss2029/WORK/PyGMIN/examples/amber/coords.inpcrd')
# load existing database
from pygmin.storage import Database
dbcurr = Database(db="/home/ss2029/WORK/PyGMIN/examples/amber/aladipep.db")
coords = sysAmb.get_random_configuration()
aa = sysAmb.get_metric_tensor(coords)
exit()
# ------- TEST gui
from pygmin.gui import run as gr
gr.run_gui(sysAmb)
# ------ Test potential
sysAmb.test_potential('coords.pdb')
# ------ BH
sysAmb.test_BH(dbcurr)
# ------- Connect runs
sysAmb.test_connect(dbcurr)
# ------- Disconn graph
sysAmb.test_disconn_graph(dbcurr)
# ------- Test mindist
sysAmb.test_mindist( dbcurr)
dlg.exec_()
self.natoms = dlg.natoms()
if dlg.result() == QtGui.QDialog.Rejected:
raise BaseException("Aborted parameter dialog")
super(LJSystem, self).__init__(self.natoms)
def get_optim_spawner(self, coords1, coords2):
from pygmin.systems.spawn_OPTIM import SpawnOPTIM_LJ
import os
# # TODO: this should be passable somehow
# optim = os.path.expanduser("~")+"/git/OPTIM/source/build/OPTIM"
## optim = "OPTIM"
optim = config.get("exec", "OPTIM")
optim = os.path.expandvars(os.path.expanduser(optim))
print "optim executable", optim
return SpawnOPTIM_LJ(coords1, coords2, self, OPTIM=optim, tempdir=True)
class NewLJDialog(QtGui.QDialog,NewLJ.Ui_DialogLJSetup):
def __init__(self):
QtGui.QDialog.__init__(self)
self.setupUi(self)
def natoms(self):
return int(self.lineNatoms.text())
def nsave(self):
return int(self.lineNsave.text())
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(LJSystem)
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system"%nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
return system
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(TIP4PSystem, db="tip4p_8.sqlite")
for xx in coords:
if(i%3 == 0):
color = [1.0, 0.0, 0.0]
radius = 0.35
else:
color = [1.0, 1.0, 1.0]
radius = 0.3
if index == 2:
color = [0.5, 1.0, .5]
i+=1
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
x=xx-com
GL.glPushMatrix()
GL.glTranslate(x[0],x[1],x[2])
GLUT.glutSolidSphere(radius,30,30)
GL.glPopMatrix()
for i in xrange(self.nrigid):
color = [1.0, 0.0, 0.0]
if index == 2:
color = [0.5, 1.0, .5]
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
self.drawCylinder(coords[3*i]-com, coords[3*i+1]-com)
self.drawCylinder(coords[3*i]-com, coords[3*i+2]-com)
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(TIP4PSystem)
def run_gui(system, db=None):
import pygmin.gui.run as gr
gr.run_gui(system, db=db)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system" % nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pygmin.gui.run as gr
gr.run_gui(TIP4PSystem, db="tip4p_8.sqlite")
# create new amber system
sysAmb = AMBERSystem('/home/ss2029/WORK/PyGMIN/examples/amber/coords.prmtop', '/home/ss2029/WORK/PyGMIN/examples/amber/coords.inpcrd')
# load existing database
from pygmin.storage import Database
dbcurr = Database(db="/home/ss2029/WORK/PyGMIN/examples/amber/aladipep.db")
coords = sysAmb.get_random_configuration()
aa = sysAmb.get_metric_tensor(coords)
exit()
# ------- TEST gui
from pygmin.gui import run as gr
gr.run_gui(sysAmb)
# ------ Test potential
sysAmb.test_potential('coords.pdb')
# ------ BH
sysAmb.test_BH(dbcurr)
# ------- Connect runs
sysAmb.test_connect(dbcurr)
# ------- Disconn graph
sysAmb.test_disconn_graph(dbcurr)
# ------- Test mindist
sysAmb.test_mindist( dbcurr)
