print "initialise md"
#print md.__doc__
mdrun = md(dt, nmd, T, slist, xyz, harmonic=True, dyn=dyn, nrep=nrep, npie=8)
#mdrun = md(dt,nmd,T,slist,xyz,harmonic=True,dyn=dyn,nrep=nrep,npie=2)
#mdrun.setDyn(eph.DynMat)
#mdrun.SetSyslist(syslist)
#mdrun.SetHarm(True)
#mdrun.SetMD(dt,nmd)
#mdrun.SetT(T)
#-------------------------------------------------------------------------------------
#initialise siesta run
#def __init__(self,label,xyz,cell,mesh=100.,dmtol=0.001,constraints=[],lunit="Ang",eunit="eV"):
constraints = [[1, 25], [-75, -1]]
srun = siesta("mdrun", xyz, cell, constraints=constraints, tdir="CGrun/")
print srun.els
mdrun.AddSint(srun)
mdrun.sint.start()
#print potforce(None,N.zeros(3*len(slist)))
#mdrun.sint.quit()
#sys.exit()
#---------------------------------------------------------------------------------
#debye bath
#---------------------------------------------------------------------------------
#def __init__(self,T,cats,debye,nw,dt=None,nmd=None,ml=None,mcof=2.0,\
# gamma=None,gwl=None,K00=None,K01=None,V01=None):
# initialise a phonon bath with debye damping
# phl = phbath(300,[0,1,2,3,4,5,6,7,8,9,10,11,12],0.022,100,mdrun.dt,mdrun.nmd)
geom = cutlayers(fn[0],
nalayer=nperlayer,
nl=cut,
nr=cut,
outfile="STRUCT.fdf")
cell, xyzonly, snr, anr = geom.pbc, geom.xyz, geom.snr, geom.anr
print anr
#xyz with element labels
#for example ['Au',0,0,0]
xyz = [[PeriodicTable[a], b[0], b[1], b[2]] for (a, b) in zip(anr, xyzonly)]
print xyz
#-------------------------------------------------------------------------------------
#initialise siesta run
#def __init__(self,label,xyz,cell,mesh=100.,dmtol=0.001,constraints=[],lunit="Ang",eunit="eV"):
srun = siesta("mdrun", xyz, cell, mesh=mesh, dmtol=dmtol, tdir=SDir)
print srun.els
srun.start()
#forces...
#q is 1d array made from
#the displacement from equilibrium in unit of 0.06466 Ang.,
#which is the internal unit of md
q = N.zeros(len(xyz))
print q
srun.force(q)
srun.quit()
harmonic=False,
dyn=N.zeros((3 * natoms, 3 * natoms)),
nrep=1)
print test.xyz
#test.setDyn(eph.DynMat)
#syslist=range(len(eph.DynMat)/3)
#test.SetSyslist(syslist)
#test.SetHarm(True)
#test.SetMD(dt,nmd)
#test.SetT(T)
#-------------------------------------------------------------------------------------
#initialise siesta run
#def __init__(self,label,xyz,cell,mesh=100.,dmtol=0.001,constraints=[],lunit="Ang",eunit="eV"):
srun = siesta("test", xyz, cell, constraints=[])
print srun.els
test.AddSint(srun)
test.sint.start()
#print potforce(None,N.zeros(3*len(slist)))
#test.sint.quit()
#sys.exit()
#---------------------------------------------------------------------------------
#debye bath
#---------------------------------------------------------------------------------
#def __init__(self,T,cats,debye,nw,dt=None,nmd=None,ml=None,mcof=2.0,\
# gamma=None,gwl=None,K00=None,K01=None,V01=None):
# initialise a phonon bath with debye damping
# phl = phbath(300,[0,1,2,3,4,5,6,7,8,9,10,11,12],0.022,100,test.dt,test.nmd)
print "initialise md"
print md.__doc__
test = md(dt, nmd, T, slist, xyz, harmonic=False, dyn=eph.DynMat)
print test.xyz
#test.setDyn(eph.DynMat)
#syslist=range(len(eph.DynMat)/3)
#test.SetSyslist(syslist)
#test.SetHarm(True)
#test.SetMD(dt,nmd)
#test.SetT(T)
#-------------------------------------------------------------------------------------
#initialise siesta run
#def __init__(self,label,xyz,cell,mesh=100.,dmtol=0.001,constraints=[],lunit="Ang",eunit="eV"):
srun = siesta("test", xyz, mdmath.cell, constraints=[[1, 32], [46, -1]])
print srun.els
test.AddSint(srun)
test.sint.start()
#print potforce(None,N.zeros(3*len(slist)))
#srun.quit()
#---------------------------------------------------------------------------------
#debye bath
#---------------------------------------------------------------------------------
#def __init__(self,T,cats,debye,nw,dt=None,nmd=None,ml=None,mcof=2.0,\
# gamma=None,gwl=None,K00=None,K01=None,V01=None):
# initialise a phonon bath with debye damping
# phl = phbath(300,[0,1,2,3,4,5,6,7,8,9,10,11,12],0.022,100,test.dt,test.nmd)
# phl.gnoi()