def __generategarbagebox__(self, Nm, Nembed, L, T):
self.X = np.empty((0, 3), dtype=np.float32)
self.S = []
self.C = np.zeros((Nm, 3), dtype=np.float32)
rint = np.random.randint(len(self.solv_list), size=Nm)
self.Na = np.zeros(Nm, dtype=np.int32)
self.ctd = []
pos = 0
plc = 0
for idx, j in enumerate(rint):
if idx < Nembed:
ri = np.random.randint(len(self.solu_list), size=1)
s = self.solu_list[ri[0]]['species']
xyz = self.solu_list[ri[0]]['coordinates']
nmc = self.solu_list[ri[0]]['nmdisplacements']
frc = self.solu_list[ri[0]]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
else:
s = self.solv_list[j]['species']
xyz = self.solv_list[j]['coordinates']
nmc = self.solv_list[j]['nmdisplacements']
frc = self.solv_list[j]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
# Apply a random rotation
M = rand_rotation_matrix()
x = np.dot(x, M.T)
maxd = hdn.generatedmatsd3(x).flatten().max() / 2.0
Nf = 0
fail = True
while fail:
ctr = np.random.uniform(2.0 * maxd + self.edgepad,
L - 2.0 * maxd - self.edgepad, (3))
fail = False
for cid, c in enumerate(self.ctd):
if np.linalg.norm(c[0] - ctr) < maxd + c[1] + 10.0:
# search for atoms within r angstroms
minv = 1000.0
for xi in self.X[c[2]:c[2] + self.Na[cid], :]:
for xj in x + ctr:
dij = np.linalg.norm(xi - xj)
if dij < minv:
minv = dij
if minv < self.mindist:
fail = True
Nf += 1
if not fail:
plc += 1
#print('Added:',plc)
self.ctd.append((ctr, maxd, pos))
self.X = np.vstack([self.X, x + ctr])
self.Na[idx] = len(s)
pos += len(s)
#print('Placement Complete...',plc,'-',Nf)
self.S.extend(s)
def __generategarbagebox__(self, Nm, L, T):
self.X = np.empty((0, 3), dtype=np.float32)
self.S = []
self.C = np.zeros((Nm, 3), dtype=np.float32)
rint = np.random.randint(len(self.mols), size=Nm)
self.Na = np.zeros(Nm, dtype=np.int32)
self.ctd = []
pos = 0
plc = 0
attempts = 0
for idx, j in enumerate(rint):
if attempts >= 10000:
break
#x = self.mols[j]['coordinates']
#s = self.mols[j]['species']
s = self.mols[j]['species']
xyz = self.mols[j]['coordinates']
nmc = self.mols[j]['nmdisplacements']
frc = self.mols[j]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
# Apply a random rotation
M = rand_rotation_matrix()
x = np.dot(x, M.T)
maxd = hdn.generatedmatsd3(x).flatten().max() / 2.0
#print('after:', maxd)
fail = True
while fail and attempts < 10000:
ctr = np.random.uniform(2.0 * maxd + 1.0, L - 2.0 * maxd - 1.0,
(3))
fail = False
for cid, c in enumerate(self.ctd):
if np.linalg.norm(c[0] - ctr) < maxd + c[1] + 10.0:
# search for atoms within r angstroms
minv = 1000.0
for xi in self.X[c[2]:c[2] + self.Na[cid], :]:
for xj in x + ctr:
dij = np.linalg.norm(xi - xj)
if dij < minv:
minv = dij
if minv < 1.5:
fail = True
attempts += 1
if not fail:
plc += 1
attempts = 0
#print('Added:',plc)
self.ctd.append((ctr, maxd, pos))
self.X = np.vstack([self.X, x + ctr])
self.Na[idx] = len(s)
pos += len(s)
self.S.extend(s)
self.Na = self.Na[0:plc]
nc = pync.molecule(cnstfile, saefile, nnfdir, 0)
mol = Atoms(spc, xyz, calculator=ANI(False))
mol.calc.setnc(nc)
LBFGS(mol).run(fmax=0.00001)
vib = Vibrations(mol)
vib.run()
vib.summary()
print(xyz)
xyz = mol.get_positions().copy()
print(xyz)
nm_cr = vib.modes[6:]
Nf = 3 * len(spc) - 6
nmo = nm_cr.reshape(Nf, len(spc), 3)
fcc = np.array([
1.314580, 1.3147106, 1.3149728, 1.5161799, 1.5164505, 5.6583018, 6.7181139,
6.7187967, 6.7193842
])
gen = nm.nmsgenerator(xyz, nmo, fcc, spc, 2000.0)
N = 2000
gen_crd = np.zeros((N, len(spc), 3), dtype=np.float32)
for i in range(N):
gen_crd[i] = gen.get_random_structure()
hdt.writexyzfile('pynmstesting.xyz', gen_crd, spc)
ids.sort()
of = open(cdir + 'kept_data.nfo', 'w')
for i in ids:
data = l_dat[i]
f = files[i]
of.write(f + '\n')
of.flush()
#print (data)
spc = data["species"]
xyz = data["coordinates"]
nmc = data["nmdisplacements"]
frc = data["forceconstant"]
nms = nmt.nmsgenerator(xyz, nmc, frc, spc, T, minfc=1.0E-2)
conformers = []
for i in range(Ngen):
conformers.append(nms.get_random_structure())
conformers = np.stack(conformers)
nc.setConformers(confs=conformers, types=list(spc))
Ecmp = nc.energy() # this generates AEVs
aevs = np.empty([Ngen, len(rcatoms) * aevsize])
for m in range(Ngen):
for j, a in enumerate(rcatoms):
aevs[m, j * aevsize:(j + 1) * aevsize] = nc.atomicenvironments(
a, m).copy()
def normal_mode_sampling(self, T, Ngen, Nkep, maxd, sig, gpuid):
of = open(self.ldtdir + self.datdir + '/info_data_nms.nfo', 'w')
aevsize = self.netdict['aevsize']
anicv = aat.anicrossvalidationconformer(self.netdict['cnstfile'],
self.netdict['saefile'],
self.netdict['nnfprefix'],
self.netdict['num_nets'],
[gpuid], False)
dc = aat.diverseconformers(self.netdict['cnstfile'],
self.netdict['saefile'],
self.netdict['nnfprefix'] + '0/networks/',
aevsize, gpuid, False)
Nkp = 0
Nkt = 0
Ntt = 0
idx = 0
for di, id in enumerate(self.idir):
of.write(
str(di) + ' of ' + str(len(self.idir)) + ') dir: ' + str(id) +
'\n')
#print(di,'of',len(self.idir),') dir:', id)
files = os.listdir(id)
files.sort()
Nk = 0
Nt = 0
for fi, f in enumerate(files):
print(f)
data = hdt.read_rcdb_coordsandnm(id + f)
#print(id+f)
spc = data["species"]
xyz = data["coordinates"]
nmc = data["nmdisplacements"]
frc = data["forceconstant"]
if "charge" in data and "multip" in data:
chg = data["charge"]
mlt = data["multip"]
else:
chg = "0"
mlt = "1"
nms = nmt.nmsgenerator(xyz,
nmc,
frc,
spc,
T,
minfc=5.0E-2,
maxd=maxd)
conformers = nms.get_Nrandom_structures(Ngen)
if conformers.shape[0] > 0:
if conformers.shape[0] > Nkep:
ids = dc.get_divconfs_ids(conformers, spc, Ngen, Nkep,
[])
conformers = conformers[ids]
sigma = anicv.compute_stddev_conformations(conformers, spc)
sid = np.where(sigma > sig)[0]
Nt += sigma.size
Nk += sid.size
if 100.0 * sid.size / float(Ngen) > 0:
Nkp += sid.size
cfn = f.split('.')[0].split('-')[0] + '_' + str(
idx).zfill(5) + '-' + f.split('.')[0].split(
'-')[1] + '_2.xyz'
cmts = [' ' + chg + ' ' + mlt for c in range(Nk)]
hdt.writexyzfilewc(self.cdir + cfn, conformers[sid],
spc, cmts)
idx += 1
Nkt += Nk
Ntt += Nt
of.write(' -Total: ' + str(Nk) + ' of ' + str(Nt) +
' percent: ' + "{:.2f}".format(100.0 * Nk / Nt) + '\n')
of.flush()
#print(' -Total:',Nk,'of',Nt,'percent:',"{:.2f}".format(100.0*Nk/Nt))
del anicv
del dc
of.write('\nGrand Total: ' + str(Nkt) + ' of ' + str(Ntt) +
' percent: ' + "{:.2f}".format(100.0 * Nkt / Ntt) + ' Kept ' +
str(Nkp) + '\n')
#print('\nGrand Total:', Nkt, 'of', Ntt,'percent:',"{:.2f}".format(100.0*Nkt/Ntt), 'Kept',Nkp)
of.close()