def test(natoms=40, boxl=None):
import pygmin.potentials.ljpshiftfast as ljpshift
from pygmin.optimize import mylbfgs
ntypeA = int(natoms * 0.8)
rcut = 2.5
coords = np.random.uniform(-1, 1, natoms * 3) * (natoms)**(1. / 3) / 2
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
pot = makeBLJNeighborListPot(natoms, ntypeA=ntypeA, rcut=rcut, boxl=boxl)
eblj = blj.getEnergy(coords)
print "blj energy", eblj
epot = pot.getEnergy(coords)
print "mcpot energy", epot
print "difference", (epot - eblj) / eblj
ret1 = mylbfgs(coords, blj, iprint=-11)
np.savetxt("out.coords", ret1.coords)
print "energy from quench1", ret1.energy
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "ret1 evaluated in both potentials", pot.getEnergy(
ret1.coords), blj.getEnergy(ret1.coords)
print "ret2 evaluated in both potentials", pot.getEnergy(
ret2.coords), blj.getEnergy(ret2.coords)
coords = ret1.coords
e1, g1 = blj.getEnergyGradient(coords)
e2, g2 = pot.getEnergyGradient(coords)
print "energy difference from getEnergyGradient", (e2 - e1)
print "largest gradient difference", np.max(np.abs(g2 - g1))
print "rms gradients", np.linalg.norm(g1) / np.sqrt(
len(g1)), np.linalg.norm(g2) / np.sqrt(len(g1))
for subpot in pot.potentials:
nl = subpot.neighborList
print "number of times neighbor list was remade", nl.buildcount, "out of", nl.count
if False:
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(np.reshape(coords, [-1, 3]), "A", 1)
pym.draw_spheres(np.reshape(ret1.coords, [-1, 3]), "A", 2)
pym.draw_spheres(np.reshape(ret2.coords, [-1, 3]), "A", 3)
except ImportError:
print "Could not draw using pymol, skipping this step"
def makeBLJNeighborListPot(natoms, ntypeA=None, rcut=2.5, boxl=None):
"""
recreate the binary lj with atom typea A,B from 3 interaction lists AA, BB, AB
"""
print "making BLJ neighborlist potential", natoms, ntypeA, rcut, boxl
#rcut = 2.5
#natoms = 40
if ntypeA is None:
ntypeA = int(natoms * 0.8)
Alist = range(ntypeA)
Blist = range(ntypeA, natoms)
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut)
ljAA = LJ(eps=blj.AA.eps,
sig=blj.AA.sig,
rcut=rcut * blj.AA.sig,
boxl=boxl)
ljBB = LJ(eps=blj.BB.eps,
sig=blj.BB.sig,
rcut=rcut * blj.BB.sig,
boxl=boxl)
ljAB = LJ(eps=blj.AB.eps,
sig=blj.AB.sig,
rcut=rcut * blj.AB.sig,
boxl=boxl)
nlAA = NeighborListSubset(natoms, rcut, Alist, boxl=boxl)
nlBB = NeighborListSubset(natoms, rcut, Blist, boxl=boxl)
nlAB = NeighborListSubset(natoms, rcut, Alist, Blist, boxl=boxl)
potlist = [
NeighborListPotential(nlAA, ljAA),
NeighborListPotential(nlBB, ljBB),
NeighborListPotential(nlAB, ljAB)
]
mcpot = MultiComponentSystem(potlist)
return mcpot
def makeBLJNeighborListPotFreeze(natoms,
frozenlist,
ntypeA=None,
rcut=2.5,
boxl=None):
"""
create the potential object for the kob andersen binary lennard jones with frozeen particles
Parameters
----------
natoms :
number of atoms in the system
frozenlist :
list of frozen atoms
ntypeA :
number of atoms of type A. It is assumed that they have indices in [0,ntypeA]
rcut :
the cutoff for the lj potential in units of sigA
boxl :
the box length for periodic box. None for no periodic boundary conditions
"""
print "making BLJ neighborlist potential", natoms, ntypeA, rcut, boxl
#rcut = 2.5
#natoms = 40
if ntypeA is None:
ntypeA = int(natoms * 0.8)
Alist = range(ntypeA)
Blist = range(ntypeA, natoms)
frozenA = np.array([i for i in Alist if i in frozenlist])
mobileA = np.array([i for i in Alist if i not in frozenlist])
frozenB = np.array([i for i in Blist if i in frozenlist])
mobileB = np.array([i for i in Blist if i not in frozenlist])
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut)
ljAA = LJCut(eps=blj.AA.eps,
sig=blj.AA.sig,
rcut=rcut * blj.AA.sig,
boxl=boxl)
ljBB = LJCut(eps=blj.BB.eps,
sig=blj.BB.sig,
rcut=rcut * blj.BB.sig,
boxl=boxl)
ljAB = LJCut(eps=blj.AB.eps,
sig=blj.AB.sig,
rcut=rcut * blj.AB.sig,
boxl=boxl)
#ten lists in total
#nlAA_ff
#nlAA_mm
#nlAA_mf
#nlBB_ff
#nlBB_mm
#nlBB_mf
#nlAB_ff
#nlAB_mm
#nlAB_mf
#nlAB_fm
nlAA_ff = NeighborListSubsetBuild(natoms, rcut, frozenA, boxl=boxl)
nlAA_mm = NeighborListSubsetBuild(natoms, rcut, mobileA, boxl=boxl)
nlAA_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=frozenA,
boxl=boxl)
nlBB_ff = NeighborListSubsetBuild(natoms, rcut, frozenB, boxl=boxl)
nlBB_mm = NeighborListSubsetBuild(natoms, rcut, mobileB, boxl=boxl)
nlBB_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileB,
Blist=frozenB,
boxl=boxl)
nlAB_ff = NeighborListSubsetBuild(natoms,
rcut,
frozenA,
Blist=frozenB,
boxl=boxl)
nlAB_mm = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=mobileB,
boxl=boxl)
nlAB_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=frozenB,
boxl=boxl)
nlAB_fm = NeighborListSubsetBuild(natoms,
rcut,
mobileB,
Blist=frozenA,
boxl=boxl)
potlist_frozen = [
NeighborListPotentialBuild(nlAA_ff, ljAA),
NeighborListPotentialBuild(nlBB_ff, ljBB),
NeighborListPotentialBuild(nlAB_ff, ljAB)
]
potlist_mobile = [
NeighborListPotentialBuild(nlAA_mm, ljAA),
NeighborListPotentialBuild(nlAA_mf, ljAA),
NeighborListPotentialBuild(nlBB_mm, ljBB),
NeighborListPotentialBuild(nlBB_mf, ljBB),
NeighborListPotentialBuild(nlAB_mm, ljAB),
NeighborListPotentialBuild(nlAB_mf, ljAB),
NeighborListPotentialBuild(nlAB_fm, ljAB),
]
#wrap the mobile potentials so the check for whether coords needs to be updated
#can be done all at once
mobile_pot = NeighborListPotentialMulti(potlist_mobile,
natoms,
rcut,
boxl=boxl)
#wrap the mobile and frozen potentials together
mcpot = MultiComponentSystemFreeze([mobile_pot], potlist_frozen)
#finally, wrap it once more in a class that will zero the gradients of the frozen atoms
frozenpot = FreezePot(mcpot, frozenlist, natoms)
return frozenpot
if False:
coords = np.array(np.loadtxt(fname))
coords = coords.reshape(-1)
boxl = 11.05209
else:
natoms = 200
coords = np.random.uniform(-1,1,natoms*3)*(natoms)**(1./3)/2
print "max, min coords", coords.max(), coords.min()
boxl = 4
natoms = len(coords) /3
ntypeA = int(natoms*0.8)
rcut = 2.5
print "natoms", natoms, "ntypea", ntypeA
bljslow = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
blj = LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
ebljslow = bljslow.getEnergy(coords)
print "blj energy slow", ebljslow
eblj = blj.getEnergy(coords)
print "blj energy ", eblj
blj.test_potential(coords)
print ""
print "partially quenching coords"
ret1 = mylbfgs(coords, blj, iprint=-11, tol=1.)
coords = ret1.coords
ebljslow = bljslow.getEnergy(coords)
print "blj energy slow", ebljslow
eblj = blj.getEnergy(coords)
def test2():
import pygmin.potentials.ljpshiftfast as ljpshiftfast
import pygmin.potentials.ljpshift as ljpshift
from pygmin.optimize import mylbfgs
fname = "/scratch/scratch2/js850/library/cluster/spherical/1620/PTMC/q4/oneatom/cavity200-8/ts/coords1.quench"
fname = "/scratch/scratch2/js850/library/cluster/spherical/1620/PTMC/q4/oneatom/cavity200-8/ts/test.coords"
#fname = "out.coords"
if False:
coords = np.array(np.loadtxt(fname))
coords = coords.reshape(-1)
boxl = 11.05209
else:
natoms = 200
coords = np.random.uniform(-1, 1, natoms * 3) * (natoms)**(1. / 3) / 2
print "max, min coords", coords.max(), coords.min()
boxl = 5
natoms = len(coords) / 3
ntypeA = int(natoms * 0.8)
rcut = 2.5
print "natoms", natoms, "ntypea", ntypeA
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
bljfast = ljpshiftfast.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
pot = makeBLJNeighborListPot(natoms, ntypeA=ntypeA, rcut=rcut, boxl=boxl)
eblj = blj.getEnergy(coords)
print "blj energy", eblj
epot = pot.getEnergy(coords)
print "mcpot energy", epot
print "energy difference", (epot - eblj)
e1, g1 = blj.getEnergyGradient(coords)
e2, g2 = pot.getEnergyGradient(coords)
print "energy difference from getEnergyGradient", (e2 - e1)
print "largest gradient difference", np.max(np.abs(g2 - g1))
print "rms gradients", np.linalg.norm(g1) / np.sqrt(
len(g1)), np.linalg.norm(g2) / np.sqrt(len(g1))
if False:
print "quenching"
ret1 = mylbfgs(coords, blj, iprint=-11)
np.savetxt("out.coords", ret1.coords)
print "energy from quench1", ret1.energy
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "max, min quenched coords", coords.max(), coords.min()
print "ret1 evaluated in both potentials", pot.getEnergy(
ret1.coords), blj.getEnergy(ret1.coords)
print "ret2 evaluated in both potentials", pot.getEnergy(
ret2.coords), blj.getEnergy(ret2.coords)
elif True:
print "quenching"
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "max, min quenched coords", ret2.coords.max(), ret2.coords.min()
print "ret2 evaluated in both potentials", pot.getEnergy(
ret2.coords), blj.getEnergy(ret2.coords)
print "and in blj fast ", bljfast.getEnergy(
ret2.coords)