def __init__(self, datafile):
self.fdata = dict()
for df in datafile:
adl = ant.anidataloader(df)
tdata = dict()
for data in adl:
tdata.update({data['path'].split('/')[-1]: data})
adl.cleanup()
self.fdata[df.split('tsdata_')[-1].split('.h5')[0]] = tdata
def sae_linear_fitting(self, Ekey='energies', energy_unit=1.0, Eax0sum=False):
from sklearn import linear_model
print('Performing linear fitting...')
datadir = self.h5dir
sae_out = self.netdict['saefile']
smap = dict()
for i,Z in enumerate(self.netdict['atomtyp']):
smap.update({Z:i})
Na = len(smap)
files = os.listdir(datadir)
X = []
y = []
for f in files[0:20]:
print(f)
adl = pyt.anidataloader(datadir + f)
for data in adl:
# print(data['path'])
S = data['species']
if data[Ekey].size > 0:
if Eax0sum:
E = energy_unit*np.sum(np.array(data[Ekey], order='C', dtype=np.float64), axis=1)
else:
E = energy_unit*np.array(data[Ekey], order='C', dtype=np.float64)
S = S[0:data['coordinates'].shape[1]]
unique, counts = np.unique(S, return_counts=True)
x = np.zeros(Na, dtype=np.float64)
for u, c in zip(unique, counts):
x[smap[u]] = c
for e in E:
X.append(np.array(x))
y.append(np.array(e))
X = np.array(X)
y = np.array(y).reshape(-1, 1)
lin = linear_model.LinearRegression(fit_intercept=False)
lin.fit(X, y)
coef = lin.coef_
print(coef)
sae = open(sae_out, 'w')
for i, c in enumerate(coef[0]):
sae.write(next(key for key, value in smap.items() if value == i) + ',' + str(i) + '=' + str(c) + '\n')
sae.close()
print('Linear fitting complete.')
def compute_test (self, h5file):
mNa = 100
# Declare loader
adl = pyt.anidataloader(h5file)
# Declare containers
Eact = []
Ecmp = []
Nmt = 0
for data in adl:
# Extract the data
xyz = data['coordinates']
Eqm = data['energies']
spc = data['species']
xyz = xyz.reshape(Eqm.shape[0], len(spc), 3)
if xyz.shape[0] > 0:
Nm = xyz.shape[0]
Na = xyz.shape[1]
if Na < mNa:
mNa = Na
Nat = Na * Nm
Nit = int(np.ceil(Nat / 65000.0))
Nmo = int(65000 / Na)
Nmx = Nm
for j in range(0, Nit):
# Setup idicies
i1 = j * Nmo
i2 = min(j * Nmo + Nmo, Nm)
# copy array subset
Eact_t = Eqm[i1:i2]
# Set the conformers in NeuroChem
self.nc.setConformers(confs=xyz[i1:i2], types=list(spc))
Ecmp_t = self.nc.energy()
Ecmp.append(np.sum(np.power(hdn.hatokcal * Ecmp_t - hdn.hatokcal * Eact_t,2)))
Nmt = Nmt + Ecmp_t.size
#Eact.append(Eact_t)
#print(hdn.hatokcal * np.sum(np.abs(Ecmp_t-Eact_t))/float(Ecmp_t.size))
Ecmp = np.array(Ecmp, dtype=np.float64)
return np.sqrt(np.sum(Ecmp) / float(Nmt))
def check_for_outsider(okayl, chckl):
for i in chckl:
if i not in okayl:
return False
return True
dst = "/home/jujuman/Research/ANI-DATASET/h5data/gdb9-2500-bad_new.h5"
src = "/home/jujuman/Research/ANI-DATASET/GDB-09-Data/gdb9-2500-bad.h5"
#open an HDF5 for compressed storage.
#Note that if the path exists, it will open whatever is there.
dpack = pyt.datapacker(dst)
aload = pyt.anidataloader(src)
at = [
'H',
'C',
'N',
'O',
#'F',
#'S',
]
for id, data in enumerate(aload.get_roman_data()):
xyz = np.asarray(data['coordinates'], dtype=np.float32)
erg = np.asarray(data['energies'], dtype=np.float64)
spc = [str(a.decode('ascii')) for a in data['species']]
# Import pyanitools
import pyanitools as pyt
# path the the store file
store_file = '/home/jujuman/Research/ANI-DATASET/rxn_db_mig.h5'
# Declare the loader, opens the store
loader = pyt.anidataloader(store_file)
# Load the entire store into memory
loader.totalload()
# Loop over store data
for i in range(loader.size()):
data = loader.getdata(i)
print(data[0])
# Closes the store file
loader.cleanup()
path = "/home/jujuman/Research/ANI-DATASET/ANI-1_release/data/ani-1_data_c08.h5"
wkdir = '/home/jujuman/Research/CrossValidation/'
cnstfile = wkdir + 'rHCNO-4.6A_16-3.1A_a4-8.params'
saefile = wkdir + 'sae_6-31gd.dat'
#-------------------------------------------
# Build networks
nc = [
pync.conformers(cnstfile, saefile,
wkdir + 'cv_c08e_ntw_' + str(l) + '/networks/', 0)
for l in range(5)
]
# Build loader
adl = pyt.anidataloader(path)
# Load data
adl.load_node("/gdb11_s01/")
# Loop
for i in range(adl.size()):
#print(i, ' of ', adl.size())
data = adl.getdata(i)
x = data[0]
e = data[1]
s = data[2]
Nm = e.shape[0]
Na = len(s)
def __init__(self, hdf5files, saef, output, storecac, storetest, Naev):
self.xyz = []
self.frc = []
self.Eqm = []
self.spc = []
self.idx = []
self.gid = []
self.prt = []
self.Naev = Naev
self.kid = [] # list to track data kept
self.nt = [] # total conformers
self.nc = [] # total kept
self.of = open(output, 'w')
self.tf = 0
for f in hdf5files:
# Construct the data loader class
adl = pyt.anidataloader(f)
print('Loading file:', f)
# Declare test cache
if os.path.exists(storetest):
os.remove(storetest)
dpack = pyt.datapacker(storetest)
for i, data in enumerate(adl):
xyz = data['coordinates']
frc = data['forces']
eng = data['energies']
spc = data['species']
nme = data['path']
# Toss out high forces
Mv = np.max(np.linalg.norm(frc, axis=2), axis=1)
index = np.where(Mv > 1.75)[0]
indexk = np.where(Mv <= 1.75)[0]
# CLear forces
xyz = xyz[indexk]
frc = frc[indexk]
eng = eng[indexk]
idx = np.random.uniform(0.0, 1.0, eng.size)
tr_idx = np.asarray(np.where(idx < 0.99))[0]
te_idx = np.asarray(np.where(idx >= 0.99))[0]
#print(tr_idx)
if tr_idx.size > 0:
self.prt.append(nme)
self.xyz.append(
np.ndarray.astype(xyz[tr_idx], dtype=np.float32))
self.frc.append(
np.ndarray.astype(frc[tr_idx], dtype=np.float32))
self.Eqm.append(
np.ndarray.astype(eng[tr_idx], dtype=np.float64))
self.spc.append(spc)
Nd = eng[tr_idx].size
#print(Nd)
self.idx.append(np.arange(Nd))
self.kid.append(np.array([], dtype=np.int))
self.gid.append(np.array([], dtype=np.int))
self.tf = self.tf + Nd
self.nt.append(Nd)
self.nc.append(0)
# Prepare and store the test data set
if xyz[te_idx].size != 0:
#t_xyz = xyz[te_idx].reshape(te_idx.size, xyz[te_idx].shape[1] * xyz[te_idx].shape[2])
dpack.store_data(nme + '/mol' + str(i),
coordinates=xyz[te_idx],
forces=frc[te_idx],
energies=np.array(eng[te_idx]),
species=spc)
# Clean up
adl.cleanup()
# Clean up
dpack.cleanup()
self.nt = np.array(self.nt)
self.nc = np.array(self.nc)
self.ts = 0
self.vs = 0
self.Nbad = self.tf
self.saef = saef
self.storecac = storecac
]
cachev = [
cg('_valid', saef, store_dir + str(r) + '/', forcet, chargt, False)
for r in range(N)
]
testh5 = [
pyt.datapacker(store_dir + str(r) + '/testset/testset.h5')
for r in range(N)
]
Nd = np.zeros(N, dtype=np.int32)
Nbf = 0
for f, fn in enumerate(h5files):
print('Processing file(' + str(f + 1) + ' of ' + str(len(h5files)) + '):',
fn)
adl = pyt.anidataloader(fn)
To = adl.size()
Ndc = 0
Fmt = []
Emt = []
for c, data in enumerate(adl):
if True:
# Get test store name
Pn = fn.split('/')[-1].rsplit('.', 1)[0] + data['path']
# Progress indicator
sys.stdout.write("\r%d%% %s" % (int(100 * c / float(To)), Pn))
sys.stdout.flush()
ax.set_ylim([shr1, shr2])
font = {'family': 'Bitstream Vera Sans', 'weight': 'heavy', 'size': 24}
ax.set_ylabel('$E_{cmp}$', fontdict=font)
ax.set_xlabel('$E_{ref}$', fontdict=font)
# Set data fields
#h5file = '/home/jujuman/Research/SingleNetworkTest/cache02/testset/testset.h5'
h5file = '/home/jujuman/Research/DataReductionMethods/models/cache/testset/testset.h5'
#h5file = '/home/jujuman/Research/ANI-DATASET/h5data/ani-gdb-c03.h5'
# Declare loader
adl = pyt.anidataloader(h5file)
nl = adl.get_group_list()
print(nl)
#node = "gdb11_s10"
#Network 1 Files
#wkdir = '/home/jujuman/Scratch/Dropbox/ChemSciencePaper.AER/networks/ANI-SN_CHNOSF-1/'
wkdir = '/home/jujuman/Research/DataReductionMethods/models/train_c08f/'
#wkdir = '/home/jujuman/Dropbox/ChemSciencePaper.AER/networks/ANI-c08f-ntwk/'
#wkdir = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/train_08_9/'
#wkdir = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/train_01/'
cnstfile = wkdir + 'rHCNO-4.6A_16-3.1A_a4-8.params'
saefile = wkdir + 'sae_6-31gd.dat'
def build_strided_training_cache(self,
Nblocks,
Nvalid,
Ntest,
build_test=True,
build_valid=False,
forces=True,
grad=False,
Fkey='forces',
forces_unit=1.0,
Ekey='energies',
energy_unit=1.0,
Eax0sum=False,
rmhighe=True):
if not os.path.isfile(self.netdict['saefile']):
self.sae_linear_fitting(Ekey=Ekey,
energy_unit=energy_unit,
Eax0sum=Eax0sum)
h5d = self.h5dir
store_dir = self.train_root + "cache-data-"
N = self.Nn
Ntrain = Nblocks - Nvalid - Ntest
if Nblocks % N != 0:
raise ValueError(
'Error: number of networks must evenly divide number of blocks.'
)
Nstride = Nblocks / N
for i in range(N):
if not os.path.exists(store_dir + str(i)):
os.mkdir(store_dir + str(i))
if build_test:
if os.path.exists(store_dir + str(i) + '/../testset/testset' +
str(i) + '.h5'):
os.remove(store_dir + str(i) + '/../testset/testset' +
str(i) + '.h5')
if not os.path.exists(store_dir + str(i) + '/../testset'):
os.mkdir(store_dir + str(i) + '/../testset')
cachet = [
cg('_train', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
cachev = [
cg('_valid', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
if build_test:
testh5 = [
pyt.datapacker(store_dir + str(r) + '/../testset/testset' +
str(r) + '.h5') for r in range(N)
]
if build_valid:
valdh5 = [
pyt.datapacker(store_dir + str(r) + '/../testset/valdset' +
str(r) + '.h5') for r in range(N)
]
if rmhighe:
dE = []
for f in self.h5file:
adl = pyt.anidataloader(h5d + f)
for data in adl:
S = data['species']
E = data['energies']
X = data['coordinates']
Esae = hdt.compute_sae(self.netdict['saefile'], S)
dE.append((E - Esae) / np.sqrt(len(S)))
dE = np.concatenate(dE)
cidx = np.where(np.abs(dE) < 15.0)
std = np.abs(dE[cidx]).std()
men = np.mean(dE[cidx])
print(men, std, men + std)
idx = np.intersect1d(
np.where(dE >= -np.abs(15 * std + men))[0],
np.where(dE <= np.abs(11 * std + men))[0])
cnt = idx.size
print('DATADIST: ', dE.size, cnt, (dE.size - cnt),
100.0 * ((dE.size - cnt) / dE.size))
E = []
data_count = np.zeros((N, 3), dtype=np.int32)
for f in self.h5file:
print('Reading data file:', h5d + f)
adl = pyt.anidataloader(h5d + f)
for data in adl:
#print(data['path'],data['energies'].size)
S = data['species']
if data[Ekey].size > 0 and (set(S).issubset(
self.netdict['atomtyp'])):
X = np.array(data['coordinates'],
order='C',
dtype=np.float32)
#print(np.array(data[Ekey].shape),np.sum(np.array(data[Ekey], order='C', dtype=np.float64),axis=1).shape,data[Fkey].shape)
if Eax0sum:
E = energy_unit * np.sum(np.array(
data[Ekey], order='C', dtype=np.float64),
axis=1)
else:
E = energy_unit * np.array(
data[Ekey], order='C', dtype=np.float64)
if forces and not grad:
F = forces_unit * np.array(
data[Fkey], order='C', dtype=np.float32)
elif forces and grad:
F = -forces_unit * np.array(
data[Fkey], order='C', dtype=np.float32)
else:
F = 0.0 * X
if rmhighe:
Esae = hdt.compute_sae(self.netdict['saefile'], S)
ind_dE = (E - Esae) / np.sqrt(len(S))
hidx = np.union1d(
np.where(ind_dE < -(15.0 * std + men))[0],
np.where(ind_dE > (11.0 * std + men))[0])
lidx = np.intersect1d(
np.where(ind_dE >= -(15.0 * std + men))[0],
np.where(ind_dE <= (11.0 * std + men))[0])
if hidx.size > 0:
print(
' -(' + f + ':' + data['path'] +
')High energies detected:\n ',
(E[hidx] - Esae) / np.sqrt(len(S)))
X = X[lidx]
E = E[lidx]
F = F[lidx]
# Build random split index
ridx = np.random.randint(0, Nblocks, size=E.size)
Didx = [
np.argsort(ridx)[np.where(ridx == i)]
for i in range(Nblocks)
]
# Build training cache
for nid, cache in enumerate(cachet):
set_idx = np.concatenate([
Didx[((bid + nid * int(Nstride)) % Nblocks)]
for bid in range(Ntrain)
])
if set_idx.size != 0:
data_count[nid, 0] += set_idx.size
cache.insertdata(X[set_idx], F[set_idx],
E[set_idx], list(S))
# for nid,cache in enumerate(cachev):
# set_idx = np.concatenate([Didx[((1+bid+nid*int(Nstride)) % Nblocks)] for bid in range(Ntrain)])
# if set_idx.size != 0:
# data_count[nid,0]+=set_idx.size
# cache.insertdata(X[set_idx], F[set_idx], E[set_idx], list(S))
for nid, cache in enumerate(cachev):
set_idx = np.concatenate([
Didx[(Ntrain + bid + nid * int(Nstride)) % Nblocks]
for bid in range(Nvalid)
])
if set_idx.size != 0:
data_count[nid, 1] += set_idx.size
cache.insertdata(X[set_idx], F[set_idx],
E[set_idx], list(S))
if build_valid:
valdh5[nid].store_data(f + data['path'],
coordinates=X[set_idx],
forces=F[set_idx],
energies=E[set_idx],
species=list(S))
if build_test:
for nid, th5 in enumerate(testh5):
set_idx = np.concatenate([
Didx[(Ntrain + Nvalid + bid +
nid * int(Nstride)) % Nblocks]
for bid in range(Ntest)
])
if set_idx.size != 0:
data_count[nid, 2] += set_idx.size
th5.store_data(f + data['path'],
coordinates=X[set_idx],
forces=F[set_idx],
energies=E[set_idx],
species=list(S))
# Save train and valid meta file and cleanup testh5
for t, v in zip(cachet, cachev):
t.makemetadata()
v.makemetadata()
if build_test:
for th in testh5:
th.cleanup()
if build_valid:
for vh in valdh5:
vh.cleanup()
print(' Train ', ' Valid ', ' Test ')
print(data_count)
print('Training set built.')
def __init__(self, hdf5files, saef, storecac, storetest):
self.xyz = []
self.Eqm = []
self.spc = []
self.idx = []
self.prt = []
self.kid = [] # list to track data kept
self.nt = [] # total conformers
self.nc = [] # total kept
self.tf = 0
for f in hdf5files:
# Construct the data loader class
adl = pyt.anidataloader(f)
# Declare test cache
if os.path.exists(storetest):
os.remove(storetest)
dpack = pyt.datapacker(storetest)
for i, data in enumerate(adl):
xyz = np.array_split(data['coordinates'], 10)
eng = np.array_split(data['energies'], 10)
spc = data['species']
nme = data['parent']
self.prt.append(nme)
self.xyz.append( np.concatenate(xyz[0:9]) )
self.Eqm.append( np.concatenate(eng[0:9]) )
self.spc.append(spc)
Nd = np.concatenate(eng[0:9]).shape[0]
self.idx.append( np.arange(Nd) )
self.kid.append( np.array([], dtype=np.int) )
self.tf = self.tf + Nd
self.nt.append(Nd)
self.nc.append(0)
# Prepare and store the test data set
if xyz[9].size != 0:
t_xyz = xyz[9].reshape(xyz[9].shape[0], xyz[9].shape[1] * xyz[9].shape[2])
dpack.store_data(nme + '/mol' + str(i), coordinates=t_xyz, energies=np.array(eng[9]), species=spc)
# Clean up
adl.cleanup()
# Clean up
dpack.cleanup()
self.nt = np.array(self.nt)
self.nc = np.array(self.nc)
self.ts = 0
self.vs = 0
self.Nbad = self.tf
self.saef = saef
self.storecac = storecac
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0002.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0003.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0004.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0005.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0006.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0007.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0008.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0009.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0010.h5',
'/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0605.0001.0011.h5',
]
r = re.compile('(.+?)(\d+?)')
comb = dict()
for h5 in h5_list:
adl = pyt.anidataloader(h5)
for data in adl:
key = data['path'].split('_')[1].split('/')[0]
items = r.findall(key)
#print(key, items, sorted(items))
#print(data.keys())
if key in comb:
comb[key].append(data)
else:
comb[key] = [data]
print(len(list(comb.keys())))
for k in comb.keys():
data = comb[k]
data_new = dict()
data_new['energies'] = data
import numpy as np
import hdnntools as gt
import pyanitools as pyt
import os
lfile = '/home/jujuman/DataTesting/gdb9-2500-div-dim.h5'
sfile = '/home/jujuman/DataTesting/gdb9-2500-div-dim_35.h5'
if os.path.exists(sfile):
os.remove(sfile)
adl = pyt.anidataloader(lfile)
dpk = pyt.datapacker(sfile)
for i,x in enumerate(adl):
print(i)
xyz = np.asarray(x['coordinates'],dtype=np.float32)
erg = x['energies']
spc = x['species']
dpk.store_data('/gdb-09-DIV/mol'+str(i), coordinates=xyz.reshape(erg.shape[0],len(spc)*3), energies=erg, species=spc)
adl.cleanup()
dpk.cleanup()
def MAE(act, pre):
N = act.shape[0]
e = (np.abs(pre - act)).sum()
return e / float(N)
# Set required files for pyNeuroChem
anipath = '/home/jujuman/Research/QM-7TEST/tester/ANI-QM7-ntwk'
cnstfile = anipath + '/rHCNOS-5.0A_16-3.1A_a4-8.params'
saefile = anipath + '/../sae_6-31gd.dat'
nnfdir = anipath + '/networks/'
path = "/home/jujuman/Scratch/Research/QM-7TEST/QM7-test-ho.h5"
datas = pyt.anidataloader(path)
datas.totalload()
# Construct pyNeuroChem class
nc = pync.conformers(cnstfile, saefile, nnfdir, 0)
Ea = np.zeros(datas.size())
Ec = np.zeros(datas.size())
for i in range(datas.size()):
print(i, ' of ', datas.size())
data = datas.getdata(i)
x = data[0]
e = data[1]
model = Net(dims).to('cuda')
model.load_state_dict(torch.load(args.model))
optimizer = optim.SGD(model.parameters(), lr=args.lr)
scheduler = optim.lr_scheduler.StepLR(optimizer, step_size=1, gamma=0.1)
# load the data into memory (big)
mcnt = 0 #molecules
ccnt = 0 #conformers
elements = set()
examples = [] #the entire training set loaded into memory
examplesbysize = dict()
for hd5file in sorted(glob.glob('*.h5')):
for data in pya.anidataloader(hd5file):
#calculate some statistics
mcnt += 1
ccnt += len(data['energies'])
elements.update(data['species'])
#molecule types and radii
types = np.array([typemap[elem] for elem in data['species']], dtype=np.float32)
radii = np.array([typeradii[int(index)] for index in types], dtype=np.float32)
sz = len(radii)
if sz not in examplesbysize:
examplesbysize[sz] = []
#create an example for every conformer
for coord, energy in zip(data['coordinates'],data['energies']):
c = molgrid.CoordinateSet(coord.astype(np.float32), types, radii,4)
def build_training_cache(self, forces=True):
store_dir = self.train_root + "cache-data-"
N = self.Nn
for i in range(N):
if not os.path.exists(store_dir + str(i)):
os.mkdir(store_dir + str(i))
if os.path.exists(store_dir + str(i) + '/../testset/testset' +
str(i) + '.h5'):
os.remove(store_dir + str(i) + '/../testset/testset' + str(i) +
'.h5')
if not os.path.exists(store_dir + str(i) + '/../testset'):
os.mkdir(store_dir + str(i) + '/../testset')
cachet = [
cg('_train', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
cachev = [
cg('_valid', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
testh5 = [
pyt.datapacker(store_dir + str(r) + '/../testset/testset' +
str(r) + '.h5') for r in range(N)
]
Nd = np.zeros(N, dtype=np.int32)
Nbf = 0
for f, fn in enumerate(self.h5file):
print(
'Processing file(' + str(f + 1) + ' of ' +
str(len(self.h5file)) + '):', fn)
adl = pyt.anidataloader(self.h5dir + fn)
To = adl.size()
Ndc = 0
Fmt = []
Emt = []
for c, data in enumerate(adl):
Pn = data['path'] + '_' + str(f).zfill(6) + '_' + str(c).zfill(
6)
# Extract the data
X = data['coordinates']
E = data['energies']
S = data['species']
# 0.0 forces if key doesnt exist
if forces:
F = data['forces']
else:
F = 0.0 * X
Fmt.append(np.max(np.linalg.norm(F, axis=2), axis=1))
Emt.append(E)
Mv = np.max(np.linalg.norm(F, axis=2), axis=1)
index = np.where(Mv > 10.5)[0]
indexk = np.where(Mv <= 10.5)[0]
Nbf += index.size
# Clear forces
X = X[indexk]
F = F[indexk]
E = E[indexk]
Esae = hdt.compute_sae(self.netdict['saefile'], S)
hidx = np.where(np.abs(E - Esae) > 10.0)
lidx = np.where(np.abs(E - Esae) <= 10.0)
if hidx[0].size > 0:
print(
' -(' + str(c).zfill(3) +
')High energies detected:\n ', E[hidx])
X = X[lidx]
E = E[lidx]
F = F[lidx]
Ndc += E.size
if (set(S).issubset(self.netdict['atomtyp'])):
# Random mask
R = np.random.uniform(0.0, 1.0, E.shape[0])
idx = np.array([interval(r, N) for r in R])
# Build random split lists
split = []
for j in range(N):
split.append([i for i, s in enumerate(idx) if s == j])
nd = len([i for i, s in enumerate(idx) if s == j])
Nd[j] = Nd[j] + nd
# Store data
for i, t, v, te in zip(range(N), cachet, cachev, testh5):
## Store training data
X_t = np.array(np.concatenate(
[X[s] for j, s in enumerate(split) if j != i]),
order='C',
dtype=np.float32)
F_t = np.array(np.concatenate(
[F[s] for j, s in enumerate(split) if j != i]),
order='C',
dtype=np.float32)
E_t = np.array(np.concatenate(
[E[s] for j, s in enumerate(split) if j != i]),
order='C',
dtype=np.float64)
if E_t.shape[0] != 0:
t.insertdata(X_t, F_t, E_t, list(S))
## Store Validation
if np.array(split[i]).size > 0:
X_v = np.array(X[split[i]],
order='C',
dtype=np.float32)
F_v = np.array(F[split[i]],
order='C',
dtype=np.float32)
E_v = np.array(E[split[i]],
order='C',
dtype=np.float64)
if E_v.shape[0] != 0:
v.insertdata(X_v, F_v, E_v, list(S))
# Print some stats
print('Data count:', Nd)
print('Data split:', 100.0 * Nd / np.sum(Nd), '%')
# Save train and valid meta file and cleanup testh5
for t, v, th in zip(cachet, cachev, testh5):
t.makemetadata()
v.makemetadata()
th.cleanup()
import pyanitools as pya
import json
fns = glob('../ANI-1_release/ani*.h5')
frames_different_molecule = []
frames_different_molecule_test = []
frames100_conf_per_mol = []
total_molecules = 22057374
seed = 2020
Nstruct = 0
for it,fn in enumerate(fns):
print(fn)
adl = pya.anidataloader(fn)
# Print the species of the data set one by one
for in_data,data in enumerate(adl):
# Extract the data
E = data['energies']
mol_in_the_block = E.shape[0]
shifts = np.random.RandomState(seed = seed).permutation(np.arange(mol_in_the_block))
frames_different_molecule.append(Nstruct + shifts[0])
frames_different_molecule_test.append(Nstruct + shifts[1])
Nstruct += mol_in_the_block
adl.cleanup()
print('Number of molecule in the dataset is ' + str(Nstruct))
frames = {'frames':frames_different_molecule,
#hdf5file = '/home/jujuman/Research/ANI-DATASET/ani-1_data_c03.h5'
storecac = '/home/jujuman/Research/SingleNetworkTest/cache06/'
saef = "/home/jujuman/Research/SingleNetworkTest/sae_6-31gd.dat"
path = "/home/jujuman/Research/SingleNetworkTest/cache06/testset/testset.h5"
# Declare data cache
cachet = cg('_train', saef, storecac, False)
cachev = cg('_valid', saef, storecac, False)
# Declare test cache
dpack = pyt.datapacker(path)
for f in hdf5files:
# Construct the data loader class
print(f)
adl = pyt.anidataloader(f[0])
print(adl.get_group_list())
# Loop over data in set
dc = 0
for i, data in enumerate(adl):
#if (i == 2):
xyz = np.array_split(data['coordinates'], 10)
eng = np.array_split(data['energies'], 10)
spc = data['species']
nme = data['parent']
#print('Parent: ', nme, eng)
dc = dc + np.concatenate(eng[0:8]).shape[0]
def build_strided_training_cache(self,
Nblocks,
Nvalid,
Ntest,
build_test=True,
forces=True,
grad=False,
Fkey='forces',
forces_unit=1.0,
Ekey='energies',
energy_unit=1.0,
Eax0sum=False):
if not os.path.isfile(self.netdict['saefile']):
self.sae_linear_fitting(Ekey=Ekey,
energy_unit=energy_unit,
Eax0sum=Eax0sum)
h5d = self.h5dir
store_dir = self.train_root + "cache-data-"
N = self.Nn
Ntrain = Nblocks - Nvalid - Ntest
if Nblocks % N != 0:
raise ValueError(
'Error: number of networks must evenly divide number of blocks.'
)
Nstride = Nblocks / N
for i in range(N):
if not os.path.exists(store_dir + str(i)):
os.mkdir(store_dir + str(i))
if build_test:
if os.path.exists(store_dir + str(i) + '/../testset/testset' +
str(i) + '.h5'):
os.remove(store_dir + str(i) + '/../testset/testset' +
str(i) + '.h5')
if not os.path.exists(store_dir + str(i) + '/../testset'):
os.mkdir(store_dir + str(i) + '/../testset')
cachet = [
cg('_train', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
cachev = [
cg('_valid', self.netdict['saefile'], store_dir + str(r) + '/',
False) for r in range(N)
]
if build_test:
testh5 = [
pyt.datapacker(store_dir + str(r) + '/../testset/testset' +
str(r) + '.h5') for r in range(N)
]
E = []
data_count = np.zeros((N, 3), dtype=np.int32)
for f in self.h5file:
adl = pyt.anidataloader(h5d + f)
for data in adl:
#print(data['path'],data['energies'].size)
S = data['species']
if data[Ekey].size > 0 and (set(S).issubset(
self.netdict['atomtyp'])):
X = np.array(data['coordinates'],
order='C',
dtype=np.float32)
if Eax0sum:
E = energy_unit * np.sum(np.array(
data[Ekey], order='C', dtype=np.float64),
axis=1)
else:
E = energy_unit * np.array(
data[Ekey], order='C', dtype=np.float64)
if forces and not grad:
F = forces_unit * np.array(
data[Fkey], order='C', dtype=np.float32)
if forces and grad:
F = -forces_unit * np.array(
data[Fkey], order='C', dtype=np.float32)
else:
F = 0.0 * X
# Build random split index
ridx = np.random.randint(0, Nblocks, size=E.size)
Didx = [
np.argsort(ridx)[np.where(ridx == i)]
for i in range(Nblocks)
]
# Build training cache
for nid, cache in enumerate(cachet):
set_idx = np.concatenate([
Didx[((bid + nid * int(Nstride)) % Nblocks)]
for bid in range(Ntrain)
])
if set_idx.size != 0:
data_count[nid, 0] += set_idx.size
cache.insertdata(X[set_idx], F[set_idx],
E[set_idx], list(S))
for nid, cache in enumerate(cachev):
set_idx = np.concatenate([
Didx[(Ntrain + bid + nid * int(Nstride)) % Nblocks]
for bid in range(Nvalid)
])
if set_idx.size != 0:
data_count[nid, 1] += set_idx.size
cache.insertdata(X[set_idx], F[set_idx],
E[set_idx], list(S))
if build_test:
for nid, th5 in enumerate(testh5):
set_idx = np.concatenate([
Didx[(Ntrain + Nvalid + bid +
nid * int(Nstride)) % Nblocks]
for bid in range(Ntest)
])
if set_idx.size != 0:
data_count[nid, 2] += set_idx.size
th5.store_data(f + data['path'],
coordinates=X[set_idx],
forces=F[set_idx],
energies=E[set_idx],
species=list(S))
# Save train and valid meta file and cleanup testh5
for t, v in zip(cachet, cachev):
t.makemetadata()
v.makemetadata()
if build_test:
for th in testh5:
th.cleanup()
print(' Train ', ' Valid ', ' Test ')
print(data_count)
print('Training set built.')
import hdnntools as hdt
import pyanitools as pyt
import os
file = '/home/jujuman/Research/DataReductionMethods/model6/model0.05me/ani_red_c06.h5'
sdir = '/home/jujuman/Research/GDB-11-AL-wB97x631gd/'
aload = pyt.anidataloader(file)
for data in aload:
X = data['coordinates']
S = data['species']
P = data['path']
parent = P.split('/')[1]
index = P.split('/')[2].split('mol')[1].zfill(7)
path = sdir+parent
if not os.path.exists(path):
os.mkdir(path)
print(path + '/' + parent + '-' + index + '.xyz','DATA:',X.shape[0])
hdt.writexyzfile(path+'/'+parent+'-'+index+'.xyz',X,S)
import os
import pickle
import pyanitools
from neurochem_calculator import NeuroChem, path
import tqdm
neurochem = NeuroChem()
# generate expect for ANI1 subset
mol_count = 0
for i in [1, 2, 3, 4]:
data_file = os.path.join(
path, '../../dataset/ani1-up_to_gdb4/ani_gdb_s0{}.h5'.format(i))
adl = pyanitools.anidataloader(data_file)
for data in tqdm.tqdm(adl, desc='ANI1: {} heavy atoms'.format(i)):
coordinates = data['coordinates'][:10, :]
pickleobj = neurochem(coordinates, data['species'])
dumpfile = os.path.join(
path, '../../tests/test_data/ANI1_subset/{}'.format(mol_count))
with open(dumpfile, 'wb') as f:
pickle.dump(pickleobj, f)
mol_count += 1
def shard_generator():
shard_size = 4096 * 64
row_idx = 0
group_idx = 0
X_cache = []
y_cache = []
w_cache = []
ids_cache = []
for hdf5file in hdf5files:
adl = pya.anidataloader(hdf5file)
for data in adl:
# Extract the data
P = data['path']
R = data['coordinates']
E = data['energies']
S = data['species']
smi = data['smiles']
if len(S) > 23:
print("skipping:", smi, "due to atom count.")
continue
# Print the data
print("Processing: ", P)
print(" Smiles: ", "".join(smi))
print(" Symbols: ", S)
print(" Coordinates: ", R.shape)
print(" Energies: ", E.shape)
Z_padded = np.zeros((23,), dtype=np.float32)
nonpadded = convert_species_to_atomic_nums(S)
Z_padded[:nonpadded.shape[0]] = nonpadded
if mode == "relative":
offset = np.amin(E)
elif mode == "atomization":
# self-interaction energies taken from
# https://github.com/isayev/ANI1_dataset README
atomizationEnergies = {
0: 0,
1: -0.500607632585,
6: -37.8302333826,
7: -54.5680045287,
8: -75.0362229210
}
offset = 0
for z in nonpadded:
offset -= atomizationEnergies[z]
elif mode == "absolute":
offset = 0
else:
raise Exception("Unsupported mode: ", mode)
for k in range(len(E)):
R_padded = np.zeros((23, 3), dtype=np.float32)
R_padded[:R[k].shape[0], :R[k].shape[1]] = R[k]
X = np.concatenate([np.expand_dims(Z_padded, 1), R_padded], axis=1)
y = E[k] - offset
if len(X_cache) == shard_size:
yield np.array(X_cache), np.array(y_cache), np.array(
w_cache), np.array(ids_cache)
X_cache = []
y_cache = []
w_cache = []
ids_cache = []
else:
X_cache.append(X)
y_cache.append(np.array(y).reshape((1,)))
w_cache.append(np.array(1).reshape((1,)))
ids_cache.append(row_idx)
row_idx += 1
groups.append(group_idx)
group_idx += 1
# flush once more at the end
if len(X_cache) > 0:
yield np.array(X_cache), np.array(y_cache), np.array(w_cache), np.array(
ids_cache)
import pyanitools as pyt
adl = pyt.anidataloader(
'/home/jujuman/Research/ANI-DATASET/h5data/r10_ccsd.h5')
for i, data in enumerate(adl):
print(data['energies'])
def shard_generator():
shard_size = 4096 * 64
row_idx = 0
group_idx = 0
X_cache = []
y_cache = []
w_cache = []
ids_cache = []
for hdf5file in hdf5files:
adl = pya.anidataloader(hdf5file)
for data in adl:
# Extract the data
P = data['path']
R = data['coordinates']
E = data['energies']
S = data['species']
smi = data['smiles']
if len(S) > 23:
print("skipping:", smi, "due to atom count.")
continue
# Print the data
print("Processing: ", P)
print(" Smiles: ", "".join(smi))
print(" Symbols: ", S)
print(" Coordinates: ", R.shape)
print(" Energies: ", E.shape)
Z_padded = np.zeros((23, ), dtype=np.float32)
nonpadded = convert_species_to_atomic_nums(S)
Z_padded[:nonpadded.shape[0]] = nonpadded
if mode == "relative":
offset = np.amin(E)
elif mode == "atomization":
# self-interaction energies taken from
# https://github.com/isayev/ANI1_dataset README
atomizationEnergies = {
0: 0,
1: -0.500607632585,
6: -37.8302333826,
7: -54.5680045287,
8: -75.0362229210
}
offset = 0
for z in nonpadded:
offset -= atomizationEnergies[z]
elif mode == "absolute":
offset = 0
else:
raise Exception("Unsupported mode: ", mode)
for k in range(len(E)):
R_padded = np.zeros((23, 3), dtype=np.float32)
R_padded[:R[k].shape[0], :R[k].shape[1]] = R[k]
X = np.concatenate([np.expand_dims(Z_padded, 1), R_padded],
axis=1)
y = E[k] - offset
if len(X_cache) == shard_size:
yield np.array(X_cache), np.array(y_cache), np.array(
w_cache), np.array(ids_cache)
X_cache = []
y_cache = []
w_cache = []
ids_cache = []
else:
X_cache.append(X)
y_cache.append(np.array(y).reshape((1, )))
w_cache.append(np.array(1).reshape((1, )))
ids_cache.append(row_idx)
row_idx += 1
groups.append(group_idx)
group_idx += 1
# flush once more at the end
if len(X_cache) > 0:
yield np.array(X_cache), np.array(y_cache), np.array(
w_cache), np.array(ids_cache)
def generate_stats(self, maxe=sys.float_info.max, forces=True, grad=False):
self.tdata = dict()
for key in self.tsfiles.keys():
print(' -Working on', key, '...')
cdata = dict({
'Eani': [],
'Edft': [],
'Fani': [],
'Fdft': [],
'dEani': [],
'dEdft': [],
'Na': [],
'Na2': [],
})
for file in self.tsfiles[key]:
adl = ant.anidataloader(file)
for i, data in enumerate(adl):
#if i > 5:
# break
if data['coordinates'].shape[0] != 0:
Eani, Fani, sig = self.compute_energyandforce_conformations(
data['coordinates'],
data['species'],
ensemble=False)
midx = np.where(
data['energies'] - data['energies'].min() < maxe /
hdt.hatokcal)[0]
Eani = Eani[:, midx]
Edft = data['energies'][midx]
Fani = Fani[:, midx, :, :]
if forces:
if grad:
Fdft = -data['forces'][midx]
else:
Fdft = data['forces'][midx]
else:
Fdft = 0.0 * data['coordinates']
#Eestd = np.std(Eani, axis=0)/np.sqrt(len(data['species']))
Eeani = np.mean(Eani, axis=0).reshape(1, -1)
Feani = np.mean(Fani, axis=0).flatten().reshape(1, -1)
Fani = Fani.reshape(Fani.shape[0], -1)
Eani = np.vstack([Eani, Eeani])
Fani = np.vstack([Fani, Feani])
Edft = hdt.hatokcal * Edft
Fdft = hdt.hatokcal * Fdft.flatten()
cdata['Na'].append(
np.full(Edft.size,
len(data['species']),
dtype=np.int32))
cdata['Eani'].append(Eani)
cdata['Edft'].append(Edft)
cdata['Fani'].append(Fani)
cdata['Fdft'].append(Fdft)
#cdata['Frmse'].append(np.sqrt(np.mean((Fani-Fdft).reshape(Fdft.shape[0], -1)**2, axis=1)))
#cdata['Frmae'].append(np.sqrt(np.mean(np.abs((Fani - Fdft).reshape(Fdft.shape[0], -1)), axis=1)))
cdata['dEani'].append(
hdt.calculateKdmat(self.Nn + 1, Eani))
cdata['dEdft'].append(hdt.calculatedmat(Edft))
cdata['Na2'].append(
np.full(cdata['dEdft'][-1].size,
len(data['species']),
dtype=np.int32))
#cdata['Erani'].append(Eani-Eani.min())
#cdata['Erdft'].append(Edft-Edft.min())
for k in ['Na', 'Na2', 'Edft', 'Fdft', 'dEdft']:
cdata[k] = np.concatenate(cdata[k])
for k in ['Eani', 'Fani', 'dEani']:
cdata[k] = np.hstack(cdata[k])
self.tdata.update({key: cdata})
import pyanitools as pya
# Set the HDF5 file containing the data
hdf5file = '../ani_gdb_s01.h5'
# Construct the data loader class
adl = pya.anidataloader(hdf5file)
# Print the species of the data set one by one
for data in adl:
# Extract the data
P = data['path']
X = data['coordinates']
E = data['energies']
S = data['species']
sm = data['smiles']
# Print the data
print("Path: ", P)
print(" Smiles: ", "".join(sm))
print(" Symbols: ", S)
print(" Coordinates: ", X)
print(" Energies: ", E, "\n")
# Closes the H5 data file
adl.cleanup()
import pyanitools as pyt
#import pyaniasetools as aat
import numpy as np
import hdnntools as hdt
import os
#import matplotlib.pyplot as plt
file_old = '/home/jsmith48/scratch/auto_al/h5files/ANI-AL-0707.0000.0408.h5'
file_new = '/home/jsmith48/scratch/auto_al/h5files_fix/ANI-AL-0707.0000.0408.h5'
print('Working on file:', file_old)
adl = pyt.anidataloader(file_old)
# Data storage
dpack = pyt.datapacker(file_new, mode='w')
for i, data in enumerate(adl):
#if i == 20:
# break
X = data['coordinates']
S = data['species']
Edft = data['energies']
path = data['path']
del data['path']
#Eani, Fani = anicv.compute_energy_conformations(X=np.array(X,dtype=np.float32),S=S)
Esae = hdt.compute_sae(
'/home/jsmith48/scratch/auto_al/modelCNOSFCl/sae_wb97x-631gd.dat', S)
