sy = np.array(t1.symbols)
dr = 0.1
rmax = 25
dct = {
'amask': [[sy == 'O', sy == 'H'], None],
'sel': [['name O', 'name H'], ['all', 'all']]
}
plots = []
for ii in range(2):
amask = dct['amask'][ii]
sel = dct['sel'][ii]
title = sel[0] + ',' + sel[1]
aa = crys.rpdf(t1, dr=dr, rmax=rmax, amask=amask, norm_vmd=False)
bb = crys.rpdf(t1, dr=dr, rmax=rmax, amask=amask, norm_vmd=True)
cc = crys.vmd_measure_gofr(t1, dr=dr, rmax=rmax, sel=sel)
plots.append(mpl.Plot())
plots[-1].ax.plot(aa[:, 0], aa[:, 1], 'b', label="g(r), norm_vmd=False")
plots[-1].ax.plot(bb[:, 0], bb[:, 1], 'r', label="g(r), norm_vmd=True")
plots[-1].ax.plot(cc[:, 0], cc[:, 1], 'g', label="g(r), vmd")
plots[-1].legend()
plots[-1].ax.set_title(title)
plots.append(mpl.Plot())
plots[-1].ax.plot(aa[:, 0], aa[:, 2], 'b', label="int, norm_vmd=False")
plots[-1].ax.plot(bb[:, 0], bb[:, 2], 'r', label="int, norm_vmd=True")
plots[-1].ax.plot(cc[:, 0], cc[:, 2], 'g', label="int, vmd")
plots[-1].legend(loc='lower right')
cell=np.identity(3)*20,
symbols=['O']*5+['H']*15)
sy = np.array(t1.symbols)
dr = 0.1
rmax = 25
dct = {'amask': [[sy=='O', sy=='H'], None],
'sel': [['name O', 'name H'], ['all', 'all']]}
plots = []
for ii in range(2):
amask = dct['amask'][ii]
sel = dct['sel'][ii]
title = sel[0] + ',' + sel[1]
aa = crys.rpdf(t1, dr=dr, rmax=rmax, amask=amask, norm_vmd=False)
bb = crys.rpdf(t1, dr=dr, rmax=rmax, amask=amask, norm_vmd=True)
cc = crys.vmd_measure_gofr(t1, dr=dr, rmax=rmax, sel=sel)
plots.append(mpl.Plot())
plots[-1].ax.plot(aa[:,0], aa[:,1], 'b', label="g(r), norm_vmd=False")
plots[-1].ax.plot(bb[:,0], bb[:,1], 'r', label="g(r), norm_vmd=True")
plots[-1].ax.plot(cc[:,0], cc[:,1], 'g', label="g(r), vmd")
plots[-1].legend()
plots[-1].ax.set_title(title)
plots.append(mpl.Plot())
plots[-1].ax.plot(aa[:,0], aa[:,2], 'b', label="int, norm_vmd=False")
plots[-1].ax.plot(bb[:,0], bb[:,2], 'r', label="int, norm_vmd=True")
plots[-1].ax.plot(cc[:,0], cc[:,2], 'g', label="int, vmd")
plots[-1].legend(loc='lower right')
def test_rpdf():
have_vmd = os.system('which vmd > /dev/null 2>&1') == 0
for name in ['rand_3d', 'aln_ibrav0_sc', 'aln_ibrav2_sc']:
print(("name: %s" % name))
dd = 'files/rpdf'
if name == 'rand_3d':
# 2 Trajectory = 2 selections
cell = np.loadtxt(pj(dd, name + '.cell.txt'))
coords_frac = [
load_old(pj(dd, name + '.coords0.txt')),
load_old(pj(dd, name + '.coords1.txt'))
]
trajs = [
crys.Trajectory(coords_frac=cf, cell=cell)
for cf in coords_frac
]
for tr in trajs:
assert tr.coords_frac.shape == (20, 10, 3)
assert tr.nstep == 20
assert tr.natoms == 10
else:
# one Structure
struct = parse.CifFile(pj(dd, name + '.cif')).get_struct()
trajs = [struct]
cell = struct.cell
ret = crys.rpdf(trajs, rmax=5.0, dr=0.05, pbc=True)
# rpdf() -- compere w/ ref
results = {
'rad': ret[:, 0],
'hist': ret[:, 1],
'num_int': ret[:, 2],
'rmax_auto': np.array(crys.rmax_smith(cell)),
}
for key, val in results.items():
print((" key: %s" % key))
ref_fn = pj(dd, "result.%s.%s.txt" % (key, name))
print((" reference file: %s" % ref_fn))
ref = np.loadtxt(ref_fn)
if doplot:
plt.figure()
plt.plot(ref, '.-', label='ref')
plt.plot(val, '.-', label='val')
plt.legend()
plt.title(key)
else:
# decimal=3 b/c ref data created w/ older implementation,
# slight numerical noise
np.testing.assert_array_almost_equal(ref, val, decimal=3)
print((" key: %s ... ok" % key))
# API
if name.startswith('aln_'):
sy = np.array(trajs[0].symbols)
ret1 = crys.rpdf(trajs, dr=0.1, amask=[sy == 'Al', sy == 'N'])
ret2 = crys.rpdf(trajs, dr=0.1, amask=['Al', 'N'])
aae(ret1, ret2)
# API:
# [traj, traj]
# [traj]
# traj
traj = crys.Trajectory(coords_frac=rand(100, 20, 3),
cell=np.identity(3) * 20,
symbols=['O'] * 5 + ['H'] * 15)
ret1 = crys.rpdf([traj, traj], rmax=5.0, dr=0.05, pbc=True)
ret2 = crys.rpdf([traj], rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret2)
ret3 = crys.rpdf(traj, rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret3)
# dmask
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask='>=2.0')
msk = ret[:, 0] >= 2.0
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask='{d}>=2.0')
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj,
rmax=5.0,
dr=0.05,
dmask='({d} >= 1.0) & ({d} <= 3.0)')
msk = (ret[:, 0] >= 1.0) & (ret[:, 0] <= 3.0)
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
if have_vmd:
# slicefirst and API
print("vmd_measure_gofr: slicefirst ...")
traj = crys.Trajectory(coords_frac=rand(100, 20, 3),
cell=np.identity(3) * 20,
symbols=['O'] * 5 + ['H'] * 15)
for first, last, step in [(0, -1, 1), (20, 80, 10)]:
ret = []
for sf in [True, False]:
print("first=%i, last=%i, step=%i, slicefirst=%s" %
(first, last, step, sf))
tmp = crys.vmd_measure_gofr(
traj,
dr=0.1,
rmax='auto',
sel=['all', 'all'],
slicefirst=sf,
first=first,
last=last,
step=step,
usepbc=1,
tmpdir=testdir,
verbose=False,
)
ret.append(tmp)
assert np.allclose(ret[0][:, 0], ret[1][:, 0])
assert np.allclose(ret[0][:, 1], ret[1][:, 1])
assert np.allclose(ret[0][:, 2], ret[1][:, 2])
# API call_vmd_measure_gofr()
trajfn = pj(testdir, 'vmd_xsf_call_vmd_measure_gofr')
data = io.write_axsf(trajfn, traj)
ret = crys.call_vmd_measure_gofr(trajfn,
dr=0.1,
rmax=10,
sel=['all', 'all'],
fntype='xsf',
first=0,
last=-1,
step=1,
usepbc=1,
datafn=None,
scriptfn=None,
logfn=None,
tmpdir=testdir,
verbose=False)
# compare results, up to L/2 = rmax_auto = 10 = rmax_smith(cell)
# all-all, hist will differ
rmax = 10
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=['all', 'all'], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=None, rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
##assert np.allclose(vmd[:-1,1], pwt[:,1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
# 2 selections, all ok
sy = np.array(traj.symbols)
vmd = crys.vmd_measure_gofr(traj,
dr=0.1,
sel=['name O', 'name H'],
rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=[sy == 'O', sy == 'H'], rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
assert np.allclose(vmd[:-1, 1], pwt[:, 1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
if doplot:
plt.show()
# all_all
amask = None
tmask = np.s_[-1]
dct['all:all:-1:-1'] = {'amask': amask, 'tmask': tmask}
tmask = np.s_[0:]
dct['all:all:0:-1'] = {'amask': amask, 'tmask': tmask}
dr = 0.1
for key, val in dct.iteritems():
print "--- %s ---" %key
print "pwtools ..."
out_pwt = \
crys.rpdf(traj,
dr=dr,
tmask=val['tmask'],
amask=val['amask'],
)
s1,s2,first,last = key.split(':')
first = int(first)
last = int(last)
if s1 != 'all':
s1 = "name %s" %s1
if s2 != 'all':
s2 = "name %s" %s2
print "vmd ..."
out_vmd = \
crys.vmd_measure_gofr(traj,
dr=dr,
rmax='auto',
sel=[s1,s2],
def test_rpdf():
have_vmd = os.system("which vmd > /dev/null 2>&1") == 0
for name in ["rand_3d", "aln_ibrav0_sc", "aln_ibrav2_sc"]:
print ("name: %s" % name)
dd = "files/rpdf"
if name == "rand_3d":
# 2 Trajectory = 2 selections
cell = np.loadtxt(pj(dd, name + ".cell.txt"))
coords_frac = [load_old(pj(dd, name + ".coords0.txt")), load_old(pj(dd, name + ".coords1.txt"))]
trajs = [crys.Trajectory(coords_frac=cf, cell=cell) for cf in coords_frac]
for tr in trajs:
assert tr.coords_frac.shape == (20, 10, 3)
assert tr.nstep == 20
assert tr.natoms == 10
else:
# one Structure
struct = parse.CifFile(pj(dd, name + ".cif")).get_struct()
trajs = [struct]
cell = struct.cell
ret = crys.rpdf(trajs, rmax=5.0, dr=0.05, pbc=True)
# rpdf() -- compere w/ ref
results = {
"rad": ret[:, 0],
"hist": ret[:, 1],
"num_int": ret[:, 2],
"rmax_auto": np.array(crys.rmax_smith(cell)),
}
for key, val in results.iteritems():
print (" key: %s" % key)
ref_fn = pj(dd, "result.%s.%s.txt" % (key, name))
print (" reference file: %s" % ref_fn)
ref = np.loadtxt(ref_fn)
if doplot:
plt.figure()
plt.plot(ref, ".-", label="ref")
plt.plot(val, ".-", label="val")
plt.legend()
plt.title(key)
else:
# decimal=3 b/c ref data created w/ older implementation,
# slight numerical noise
np.testing.assert_array_almost_equal(ref, val, decimal=3)
print (" key: %s ... ok" % key)
# API
if name.startswith("aln_"):
sy = np.array(trajs[0].symbols)
ret1 = crys.rpdf(trajs, dr=0.1, amask=[sy == "Al", sy == "N"])
ret2 = crys.rpdf(trajs, dr=0.1, amask=["Al", "N"])
aae(ret1, ret2)
# API:
# [traj, traj]
# [traj]
# traj
traj = crys.Trajectory(coords_frac=rand(100, 20, 3), cell=np.identity(3) * 20, symbols=["O"] * 5 + ["H"] * 15)
ret1 = crys.rpdf([traj, traj], rmax=5.0, dr=0.05, pbc=True)
ret2 = crys.rpdf([traj], rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret2)
ret3 = crys.rpdf(traj, rmax=5.0, dr=0.05, pbc=True)
aae(ret1, ret3)
# dmask
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask=">=2.0")
msk = ret[:, 0] >= 2.0
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask="{d}>=2.0")
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
ret = crys.rpdf(traj, rmax=5.0, dr=0.05, dmask="({d} >= 1.0) & ({d} <= 3.0)")
msk = (ret[:, 0] >= 1.0) & (ret[:, 0] <= 3.0)
imsk = np.invert(msk)
assert (ret[msk, 1] > 0.0).any()
assert (ret[imsk, 1] == 0.0).all()
if have_vmd:
# slicefirst and API
print "vmd_measure_gofr: slicefirst ..."
traj = crys.Trajectory(coords_frac=rand(100, 20, 3), cell=np.identity(3) * 20, symbols=["O"] * 5 + ["H"] * 15)
for first, last, step in [(0, -1, 1), (20, 80, 10)]:
ret = []
for sf in [True, False]:
print "first=%i, last=%i, step=%i, slicefirst=%s" % (first, last, step, sf)
tmp = crys.vmd_measure_gofr(
traj,
dr=0.1,
rmax="auto",
sel=["all", "all"],
slicefirst=sf,
first=first,
last=last,
step=step,
usepbc=1,
tmpdir=testdir,
verbose=False,
)
ret.append(tmp)
assert np.allclose(ret[0][:, 0], ret[1][:, 0])
assert np.allclose(ret[0][:, 1], ret[1][:, 1])
assert np.allclose(ret[0][:, 2], ret[1][:, 2])
# API call_vmd_measure_gofr()
trajfn = pj(testdir, "vmd_xsf_call_vmd_measure_gofr")
data = io.write_axsf(trajfn, traj)
ret = crys.call_vmd_measure_gofr(
trajfn,
dr=0.1,
rmax=10,
sel=["all", "all"],
fntype="xsf",
first=0,
last=-1,
step=1,
usepbc=1,
datafn=None,
scriptfn=None,
logfn=None,
tmpdir=testdir,
verbose=False,
)
# compare results, up to L/2 = rmax_auto = 10 = rmax_smith(cell)
# all-all, hist will differ
rmax = 10
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=["all", "all"], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=None, rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
##assert np.allclose(vmd[:-1,1], pwt[:,1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
# 2 selections, all ok
sy = np.array(traj.symbols)
vmd = crys.vmd_measure_gofr(traj, dr=0.1, sel=["name O", "name H"], rmax=10)
pwt = crys.rpdf(traj, dr=0.1, amask=[sy == "O", sy == "H"], rmax=10)
assert np.allclose(vmd[:-1, 0], pwt[:, 0]) # rad
assert np.allclose(vmd[:-1, 1], pwt[:, 1]) # hist
assert np.allclose(vmd[:-1, 2], pwt[:, 2]) # num_int
if doplot:
plt.show()
np.random.seed(3)
natoms_O = 10
natoms_H = 3
symbols = ['O'] * natoms_O + ['H'] * natoms_H
coords_in = np.random.rand(natoms_H + natoms_O, 3, 30)
cell = np.identity(3) * 10
sy = np.array(symbols)
msk1 = sy == 'O'
msk2 = sy == 'H'
coords = [coords_in[msk1, ..., 10:], coords_in[msk1, ..., 10:]]
np.savetxt(pj(dd, name + '.cell.txt'), cell)
io.writetxt(pj(dd, name + '.coords0.txt'), coords[0])
io.writetxt(pj(dd, name + '.coords1.txt'), coords[1])
else:
pp = parse.CifFile(pj(dd, name + '.cif'))
pp.parse()
coords = pp.coords
cell = pp.cell
rad, hist, num_int = crys.rpdf(
coords,
rmax=5.0,
cell=cell,
dr=0.05,
pbc=True,
)
np.savetxt(pj(dd, "result.rad." + name + ".txt"), rad)
np.savetxt(pj(dd, "result.hist." + name + ".txt"), hist)
np.savetxt(pj(dd, "result.num_int." + name + ".txt"), num_int)
np.savetxt(pj(dd, "result.rmax_auto." + name + ".txt"),
[crys.rmax_smith(cell)])
if __name__ == "__main__":
for name in ["rand_3d", "aln_ibrav0_sc", "aln_ibrav2_sc"]:
dd = "../files/rpdf"
if name == "rand_3d":
# important!
np.random.seed(3)
natoms_O = 10
natoms_H = 3
symbols = ["O"] * natoms_O + ["H"] * natoms_H
coords_in = np.random.rand(natoms_H + natoms_O, 3, 30)
cell = np.identity(3) * 10
sy = np.array(symbols)
msk1 = sy == "O"
msk2 = sy == "H"
coords = [coords_in[msk1, ..., 10:], coords_in[msk1, ..., 10:]]
np.savetxt(pj(dd, name + ".cell.txt"), cell)
io.writetxt(pj(dd, name + ".coords0.txt"), coords[0])
io.writetxt(pj(dd, name + ".coords1.txt"), coords[1])
else:
pp = parse.CifFile(pj(dd, name + ".cif"))
pp.parse()
coords = pp.coords
cell = pp.cell
rad, hist, num_int = crys.rpdf(coords, rmax=5.0, cell=cell, dr=0.05, pbc=True)
np.savetxt(pj(dd, "result.rad." + name + ".txt"), rad)
np.savetxt(pj(dd, "result.hist." + name + ".txt"), hist)
np.savetxt(pj(dd, "result.num_int." + name + ".txt"), num_int)
np.savetxt(pj(dd, "result.rmax_auto." + name + ".txt"), [crys.rmax_smith(cell)])
#------------------------------------------------------------------------
# plotting
#------------------------------------------------------------------------
# For all structs, calculate rmax=5 (= rmax_auto for aln_ibrav0_sc for a
# 2x2x2 cell) and rmax = 20 as well as pbc=True, False. Plot for 1 struct.
plots = {}
for struct in structs.values():
cc = iter(['b', 'r', 'g', 'm'])
mm = iter(['v', '^', '+', 'x'])
for rmax in [5, 20]:
for pbc in [True, False]:
rmax_auto = crys.rmax_smith(struct.cell)
out = \
crys.rpdf(struct,
rmax=rmax,
dr=0.05,
pbc=pbc)
pl = Plot()
pl.name = struct.fnbase
pl.rad = out[:,0]
pl.hist = out[:,1]
pl.num_int = out[:,2]
pl.color = next(cc)
pl.marker = next(mm)
pl.leg_label = "pbc=%s, rmax=%i, rmax_auto=%.1f" %(pbc, rmax,
rmax_auto)
plots["%s-%i-%s" %(struct.fnbase, rmax, pbc)] = pl
name='aln_ibrav0_sc'
plot_pl(plots[name + "-5-True"], plots[name + "-20-True"])
plot_pl(plots[name + "-5-False"], plots[name + "-20-False"])
# all_all
amask = None
tmask = np.s_[-1]
dct['all:all:-1:-1'] = {'amask': amask, 'tmask': tmask}
tmask = np.s_[0:]
dct['all:all:0:-1'] = {'amask': amask, 'tmask': tmask}
dr = 0.1
for key, val in dct.items():
print("--- %s ---" % key)
print("pwtools ...")
out_pwt = \
crys.rpdf(traj,
dr=dr,
tmask=val['tmask'],
amask=val['amask'],
)
s1, s2, first, last = key.split(':')
first = int(first)
last = int(last)
if s1 != 'all':
s1 = "name %s" % s1
if s2 != 'all':
s2 = "name %s" % s2
print("vmd ...")
out_vmd = \
crys.vmd_measure_gofr(traj,
dr=dr,
rmax='auto',
sel=[s1,s2],
#------------------------------------------------------------------------
# plotting
#------------------------------------------------------------------------
# For all structs, calculate rmax=5 (= rmax_auto for aln_ibrav0_sc for a
# 2x2x2 cell) and rmax = 20 as well as pbc=True, False. Plot for 1 struct.
plots = {}
for struct in structs.itervalues():
cc = iter(['b', 'r', 'g', 'm'])
mm = iter(['v', '^', '+', 'x'])
for rmax in [5, 20]:
for pbc in [True, False]:
rmax_auto = crys.rmax_smith(struct.cell)
out = \
crys.rpdf(struct,
rmax=rmax,
dr=0.05,
pbc=pbc)
pl = Plot()
pl.name = struct.fnbase
pl.rad = out[:,0]
pl.hist = out[:,1]
pl.num_int = out[:,2]
pl.color = cc.next()
pl.marker = mm.next()
pl.leg_label = "pbc=%s, rmax=%i, rmax_auto=%.1f" %(pbc, rmax,
rmax_auto)
plots["%s-%i-%s" %(struct.fnbase, rmax, pbc)] = pl
name='aln_ibrav0_sc'
plot_pl(plots[name + "-5-True"], plots[name + "-20-True"])
plot_pl(plots[name + "-5-False"], plots[name + "-20-False"])
