def generate_h5(self, path):
# open an HDF5 for compressed storage.
# Note that if the path exists, it will open whatever is there.
dpack = pyt.datapacker(path)
d = self.ldtdir + self.datdir + '/data/'
files = [f for f in os.listdir(d) if ".dat" in f]
files.sort()
Nf = len(files)
Nd = 0
for n, f in enumerate(files):
#print(d + f)
L = file_len(d + f)
if L >= 4:
#print(d + f)
data = hdt.readncdatall(d + f)
if 'energies' in data:
Ne = data['energies'].size
Nd += Ne
f = f.rsplit("-", 1)
fn = f[0] + "/mol" + f[1].split(".")[0]
dpack.store_data(fn, **data)
dpack.cleanup()
Nd = 0
Nf = 0
for i, d in enumerate(dtdirs):
files = [f for f in os.listdir(d) if ".dat" in f]
files.sort()
Nf += len(files)
for n, f in enumerate(files):
L = file_len(d + f)
if L >= 4:
print(d + f)
data = hdn.readncdatall(d + f)
#ridx = np.random.rand(data['energies'].size)
#ridx = np.where(ridx < 0.2)
#data['energies'] = data['energies'][ridx]
#data['forces'] = data['forces'][ridx]# / (0.52917724900001*0.52917724900001)
#data['coordinates'] = data['coordinates'][ridx]
Ne = data['energies'].size
Nd += Ne
f = f.rsplit("-", 1)
#print(f)
fn = f[0] + '-' + str(i).zfill(3) + "/mol" + f[1].split(".")[0]
molfile = '/home/jujuman/Research/MD_TEST/trim.dat'
wkdir = '/home/jujuman/Scratch/Research/DataReductionMethods/model6r/model-gdb01-06_red03-08/cv1/train4/'
cnstfile = wkdir + '../rHCNO-4.6A_16-3.1A_a4-8.params'
saefile = wkdir + '../sae_6-31gd.dat'
nnfdir = wkdir + 'networks/'
wkdir = '/home/jujuman/Gits/ANI-Networks/networks/ANI-c08f-ntwk-cv/'
cnstfile = wkdir + 'rHCNO-4.6A_16-3.1A_a4-8.params'
saefile = wkdir + 'sae_6-31gd.dat'
nnfdir = wkdir + 'cv_train_4/networks/'
nc = pync.conformers(cnstfile, saefile, nnfdir, 0, False)
data = hdt.readncdatall(molfile)
Edft = data["energies"]
nc.setConformers(confs=data["coordinates"], types=data["species"])
Eani = nc.energy()
print(Eani)
import matplotlib.pyplot as plt
plt.plot(hdt.hatokcal * (Edft), label='DFT')
plt.plot(hdt.hatokcal * (Eani), label='ANI')
plt.ylabel('$E_t$ (kcal/mol)')
plt.xlabel('Frame')
plt.legend(bbox_to_anchor=(0.01, 0.99), loc=2, borderaxespad=0., fontsize=14)