def getValues():
isize,index,grpnames=rd_index(idxfile,2)
if isize[0]!=4 or isize[1]!=4:
print "Index sizes are not OK! Must be equal 4"
sys.exit(1)
traj=Trajectory(trajfile)
values = []
for positions,step,time,matrix,prec,box in traj:
sys.stdout.write("Step: %d \tTime: %6.3f\r"%(step,time))
donorpos,donorvec=getPosVec(positions,index[0])
acceptorpos,acceptorvec=getPosVec(positions,index[1])
R=norm(donorpos-acceptorpos)
Rvec=(donorpos-acceptorpos)/R
kappa=(donorvec*acceptorvec).sum()-3*((donorvec*Rvec).sum()*(acceptorvec*Rvec).sum())
kappasq=kappa*kappa
values.append((time,R,kappasq))
return array(values)
def getValues():
isize, index, grpnames = rd_index(idxfile, 2)
if isize[0] != 4 or isize[1] != 4:
print "Index sizes are not OK! Must be equal 4"
sys.exit(1)
traj = Trajectory(trajfile)
values = []
for positions, step, time, matrix, prec, box in traj:
sys.stdout.write("Step: %d \tTime: %6.3f\r" % (step, time))
donorpos, donorvec = getPosVec(positions, index[0])
acceptorpos, acceptorvec = getPosVec(positions, index[1])
R = norm(donorpos - acceptorpos)
Rvec = (donorpos - acceptorpos) / R
kappa = (donorvec * acceptorvec).sum() - 3 * (
(donorvec * Rvec).sum() * (acceptorvec * Rvec).sum())
kappasq = kappa * kappa
values.append((time, R, kappasq))
return array(values)
def main():
parser = OptionParser()
#parser.add_option("-s",metavar="FILE",help="Reference Structure file",default="topol.tpr")
parser.add_option("-n", metavar="FILE", help="Index file")
parser.add_option("-f",
metavar="FILE",
help="Trajectory with coordinates, velocies, and forces")
parser.add_option("-x", metavar="FILE", help="Trajectory with coordinates")
parser.add_option("-v", metavar="FILE", help="Trajectory with velocities")
parser.add_option("-k", metavar="FILE", help="Trajectory with forces")
parser.add_option("-o", metavar="FILE", help="Output", default="corr.dat")
parser.add_option("-r", metavar="FILE", help="Output", default="rot.dat")
(options, args) = parser.parse_args()
#open files
#sf = tpxfile(options.s)
#read index
if options.n:
isize, idx, iname = rd_index(options.n, 1)
print("Using group %s with %s atoms" % (iname[0], isize[0]))
idx = idx[0]
if not options.f and not (options.x and options.v and options.k):
print(
"Requires either one trajectory containing all input (-f) or three (-x, -v, -f)"
)
sys.exit(1)
if options.f and (options.x or options.v or options.k):
print("-f cannot be used with x,v, or k")
sys.exit(1)
if options.f:
tf = gmxfile(options.f, flags=TRX_NEED_X | TRX_NEED_V | TRX_NEED_F)
natoms = tf.natoms
else:
xf = gmxfile(options.x, flags=TRX_NEED_X)
vf = gmxfile(
options.v, flags=TRX_NEED_X
) #DCD doesn't have V/F so we expect all 3 files have X field
kf = gmxfile(options.k, flags=TRX_NEED_X)
print("Warning: NAMD units are expected for input files!")
natoms = xf.natoms
tf = izip(xf, vf, kf)
if natoms != vf.natoms or natoms != kf.natoms:
print("Number of atoms doesn't match between files!")
sys.exit(1)
if (natoms % 3 != 0):
print(
"This program only supports water. Number of atoms has to be multiple of 3."
)
sys.exit(1)
temp_v = []
temp_x = []
temp_f = []
trn_v = N.empty((nP, natoms / 3, 3, 3), dtype=N_real)
trn_x = N.empty((nP, natoms / 3, 3, 3), dtype=N_real)
for i, frm in enumerate(tf):
if not options.f:
frm_t = frm
class frm: #convert tuple into attributes
x = frm_t[0].x
v = frm_t[1].x * 20.45482706
f = frm_t[2].x * (100 / 4.184)
if options.n:
frm_x = frm.x[idx]
frm_v = frm.v[idx]
frm_f = frm.f[idx]
else:
frm_x = frm.x
frm_v = frm.v
frm_f = frm.f
frm_v = frm_v.reshape(-1, 3, 3)
frm_x = frm_x.reshape(-1, 3, 3)
frm_f = frm_f.reshape(-1, 3, 3)
temp_v += [frm_v.copy()]
temp_x += [frm_x.copy()]
temp_f += [frm_f.copy()]
temp_v = temp_v[-3:]
temp_x = temp_x[-3:]
temp_f = temp_f[-3:]
if i % ds != 2: continue #assumes ds>=3,
if __debug__:
a = temp_x[1]
b = temp_x[0] + temp_v[1] * dt
#print(temp_v[1]*dt)
#print(temp_x[0])
#idx=N.abs(a-b).max(axis=1).max(axis=1)>.0005
#print(a.shape,temp_v[1].shape)
#print(idx)
#print(a[idx])
#print(b[idx])
N.testing.assert_almost_equal(
a, b, decimal=2,
verbose=True) #low accuracy dominated by pressure coupling
i = i // ds
trn_v[i] = .5 * (temp_v[1] + temp_v[2]) - dt / 16 / mass * (temp_f[2] -
temp_f[0])
#trn_v[i] = .5*(temp_v[1]+temp_v[2])
##trn_v2 = 2*(trn_v[1:-1]+trn_v[2:])-3/2/dt*(trn_x[2:]-trn_x[:-2])
trn_x[i] = temp_x[1]
if i == nP - 1: break
if __debug__:
a = (temp_v[0] + temp_v[1]) / 2 #trn_v2[n]
b = trn_v[i]
#idx=N.abs((a-b))>.4+.2*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx = N.abs((a - b)) > .6 + .4 * N.abs(
a + b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx2 = N.abs(
(a - b)) < .1 + .05 * N.abs(a + b) #.1 .05 : 75% - 1fs: 91%
assert (N.sum(idx) / N.prod(idx2.shape) < 1 / 400)
#assert(N.sum(idx2)/N.prod(idx2.shape)>.9)
assert (N.sum(idx2) / N.prod(idx2.shape) > .70)
assert (i == nP - 1)
N.set_string_function(N.array_repr, False)
x = trn_x[0][0] #1st frame, 1st molecule
x = x - N.sum(x * mass, axis=0) / N.sum(mass)
I = inertia_tensor(x, mass)
I, evec = LA.eigh(I)
print()
print("I", I)
ic = N.array(
N.dot(x, evec), dtype=N_real
) #initial water coordinates (oriented according to I); orientation x: H1->H2, y: O->(H1+H2)/2, z: perpendicular to plane
print(trn_x.shape, trn_v.shape)
trn_w = N.empty((len(trn_v), natoms / 3, 3), dtype=N_real)
#COM
trn_x -= N.sum(trn_x * mass, axis=2).reshape(nP, natoms / 3, 1, 3) / N.sum(
mass) #reshape doesn't change shape but reinserts the summed axis
trn_v_com = trn_v - N.sum(trn_v * mass, axis=2).reshape(
nP, natoms / 3, 1, 3) / N.sum(mass)
for n in range(len(trn_v)):
trn_w[n] = compute_omega(trn_x[n], trn_v_com[n], ic, I,
mass.reshape(3))
#trn_w[n] = compute_omega_py(trn_x[n], trn_v_com[n], ic, I, mass)
trn_w = trn_w[:nP]
corr = N.apply_along_axis(
lambda a: scipy.signal.fftconvolve(a, a[::-1], 'same'),
axis=0,
arr=trn_w)
corr = corr[len(corr) / 2:] #remove negative lag
corr = norm_corr(corr)
rf = file(options.r, "w")
map(lambda x: print(x, file=rf), corr)
#if len(trn_v)%2==1: #remove last if uneven number of trn-data points
#
trn_v = trn_v[:nP] #TODO: make configurable, switch here for trn/rot
print(trn_v.shape)
if bCom:
#trn_v = trn_v.reshape((-1,natoms/3,3,3)) #group as waters
trn_v = N.mean(
trn_v * mass,
axis=2) #average over waters, now shape is: frame, mol, coor
print(trn_v.shape)
corr = N.apply_along_axis(
lambda a: scipy.signal.fftconvolve(a, a[::-1], 'same'),
axis=0,
arr=trn_v)
#corr = N.apply_along_axis(lambda a: N.correlate(a,a,'same'),axis=0,arr=trn_v) #slower identical alternative
print(corr.shape)
corr = corr[len(corr) / 2:] #remove negative lag
if bCom:
if not bNormalize:
corr /= N.sum(
mass
) #we multiplied trn with mass and because correlation is trn*trn the correlation was mass^2
else:
corr = corr.reshape(
-1, natoms / 3, 3, 3
) #frames, molecule, atoms, xyz; so that we can multiply with mass
print(corr.shape)
corr *= mass
corr = norm_corr(corr)
print(corr.shape)
of = file(options.o, "w")
map(lambda x: print(x, file=of), corr)
def main():
parser = OptionParser()
#parser.add_option("-s",metavar="FILE",help="Reference Structure file",default="topol.tpr")
parser.add_option("-n",metavar="FILE",help="Index file")
parser.add_option("-f",metavar="FILE",help="Trajectory with coordinates, velocies, and forces")
parser.add_option("-x",metavar="FILE",help="Trajectory with coordinates")
parser.add_option("-v",metavar="FILE",help="Trajectory with velocities")
parser.add_option("-k",metavar="FILE",help="Trajectory with forces")
parser.add_option("-o",metavar="FILE",help="Output",default="corr.dat")
parser.add_option("-r",metavar="FILE",help="Output",default="rot.dat")
(options, args) = parser.parse_args()
#open files
#sf = tpxfile(options.s)
#read index
if options.n:
isize,idx,iname = rd_index(options.n,1)
print("Using group %s with %s atoms"%(iname[0],isize[0]))
idx=idx[0]
if not options.f and not(options.x and options.v and options.k):
print("Requires either one trajectory containing all input (-f) or three (-x, -v, -f)")
sys.exit(1);
if options.f and (options.x or options.v or options.k):
print("-f cannot be used with x,v, or k")
sys.exit(1);
if options.f:
tf = gmxfile(options.f,flags=TRX_NEED_X|TRX_NEED_V|TRX_NEED_F)
natoms = tf.natoms
else:
xf = gmxfile(options.x,flags=TRX_NEED_X)
vf = gmxfile(options.v,flags=TRX_NEED_X) #DCD doesn't have V/F so we expect all 3 files have X field
kf = gmxfile(options.k,flags=TRX_NEED_X)
print("Warning: NAMD units are expected for input files!")
natoms = xf.natoms
tf = izip(xf,vf,kf)
if natoms!=vf.natoms or natoms!=kf.natoms:
print("Number of atoms doesn't match between files!")
sys.exit(1);
if (natoms%3!=0):
print("This program only supports water. Number of atoms has to be multiple of 3.");
sys.exit(1);
temp_v=[]
temp_x=[]
temp_f=[]
trn_v=N.empty((nP,natoms/3,3,3),dtype=N_real)
trn_x=N.empty((nP,natoms/3,3,3),dtype=N_real)
for i,frm in enumerate(tf):
if not options.f:
frm_t = frm
class frm: #convert tuple into attributes
x = frm_t[0].x
v = frm_t[1].x*20.45482706
f = frm_t[2].x*(100/4.184)
if options.n:
frm_x = frm.x[idx]
frm_v = frm.v[idx]
frm_f = frm.f[idx]
else:
frm_x = frm.x
frm_v = frm.v
frm_f = frm.f
frm_v=frm_v.reshape(-1,3,3)
frm_x=frm_x.reshape(-1,3,3)
frm_f=frm_f.reshape(-1,3,3)
temp_v += [frm_v.copy()]
temp_x += [frm_x.copy()]
temp_f += [frm_f.copy()]
temp_v = temp_v[-3:]
temp_x = temp_x[-3:]
temp_f = temp_f[-3:]
if i%ds!=2: continue #assumes ds>=3,
if __debug__:
a=temp_x[1]
b=temp_x[0]+temp_v[1]*dt
#print(temp_v[1]*dt)
#print(temp_x[0])
#idx=N.abs(a-b).max(axis=1).max(axis=1)>.0005
#print(a.shape,temp_v[1].shape)
#print(idx)
#print(a[idx])
#print(b[idx])
N.testing.assert_almost_equal(a,b,decimal=2,verbose=True) #low accuracy dominated by pressure coupling
i=i//ds
trn_v[i] = .5*(temp_v[1]+temp_v[2])-dt/16/mass*(temp_f[2]-temp_f[0])
#trn_v[i] = .5*(temp_v[1]+temp_v[2])
##trn_v2 = 2*(trn_v[1:-1]+trn_v[2:])-3/2/dt*(trn_x[2:]-trn_x[:-2])
trn_x[i] = temp_x[1]
if i==nP-1: break
if __debug__:
a=(temp_v[0]+temp_v[1])/2#trn_v2[n]
b=trn_v[i]
#idx=N.abs((a-b))>.4+.2*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx=N.abs((a-b))>.6+.4*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx2=N.abs((a-b))<.1+.05*N.abs(a+b) #.1 .05 : 75% - 1fs: 91%
assert(N.sum(idx)/N.prod(idx2.shape)<1/400)
#assert(N.sum(idx2)/N.prod(idx2.shape)>.9)
assert(N.sum(idx2)/N.prod(idx2.shape)>.70)
assert(i==nP-1)
N.set_string_function(N.array_repr,False)
x=trn_x[0][0] #1st frame, 1st molecule
x=x-N.sum(x*mass,axis=0)/N.sum(mass)
I=inertia_tensor(x,mass)
I,evec=LA.eigh(I)
print()
print("I",I)
ic = N.array(N.dot(x,evec),dtype=N_real) #initial water coordinates (oriented according to I); orientation x: H1->H2, y: O->(H1+H2)/2, z: perpendicular to plane
print(trn_x.shape,trn_v.shape)
trn_w=N.empty((len(trn_v),natoms/3,3),dtype=N_real)
#COM
trn_x -= N.sum(trn_x*mass,axis=2).reshape(nP,natoms/3,1,3)/N.sum(mass) #reshape doesn't change shape but reinserts the summed axis
trn_v_com = trn_v - N.sum(trn_v*mass,axis=2).reshape(nP,natoms/3,1,3)/N.sum(mass)
for n in range(len(trn_v)):
trn_w[n] = compute_omega(trn_x[n], trn_v_com[n], ic, I, mass.reshape(3))
#trn_w[n] = compute_omega_py(trn_x[n], trn_v_com[n], ic, I, mass)
trn_w=trn_w[:nP]
corr = N.apply_along_axis(lambda a: scipy.signal.fftconvolve(a,a[::-1],'same'),axis=0,arr=trn_w)
corr = corr[len(corr)/2:] #remove negative lag
corr=norm_corr(corr)
rf=file(options.r,"w")
map(lambda x:print(x,file=rf),corr)
#if len(trn_v)%2==1: #remove last if uneven number of trn-data points
#
trn_v=trn_v[:nP] #TODO: make configurable, switch here for trn/rot
print(trn_v.shape)
if bCom:
#trn_v = trn_v.reshape((-1,natoms/3,3,3)) #group as waters
trn_v = N.mean(trn_v*mass, axis=2) #average over waters, now shape is: frame, mol, coor
print(trn_v.shape)
corr = N.apply_along_axis(lambda a: scipy.signal.fftconvolve(a,a[::-1],'same'),axis=0,arr=trn_v)
#corr = N.apply_along_axis(lambda a: N.correlate(a,a,'same'),axis=0,arr=trn_v) #slower identical alternative
print(corr.shape)
corr = corr[len(corr)/2:] #remove negative lag
if bCom:
if not bNormalize:
corr/=N.sum(mass) #we multiplied trn with mass and because correlation is trn*trn the correlation was mass^2
else:
corr = corr.reshape(-1,natoms/3,3,3) #frames, molecule, atoms, xyz; so that we can multiply with mass
print(corr.shape)
corr *= mass
corr=norm_corr(corr)
print(corr.shape)
of=file(options.o,"w")
map(lambda x:print(x,file=of),corr)
