# Import pyNeuroChem
import pyNeuroChem as pync
import time as tm
import numpy as np
import graphtools as gt
# Set required files for pyNeuroChem
wkdir = '/home/jujuman/Dropbox/ChemSciencePaper.AER/ANI-1-ntwk/'
cnstfile = wkdir + 'rHCNO-4.6A_32-3.1A_a8-8.params'
saefile = wkdir + 'sae_6-31gd.dat'
nnfdir = wkdir + 'networks/'
# Construct pyNeuroChem class
nc = pync.pyNeuroChem(cnstfile,saefile,nnfdir,0)
xyz,typ,Na = gt.readxyz('/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_begdb/begdb-h2oclusters/xyz/4216_water10PP2.xyz')
xyz1,typ1,Na1 = gt.readxyz('/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnnts_begdb/begdb-h2oclusters/xyz/4216_water10PP2.xyz')
# Set the conformers in NeuroChem
nc.setConformers(confs=xyz,types=typ[0])
# Print some data from the NeuroChem
print( 'Number of Atoms Loaded: ' + str(nc.getNumAtoms()) )
print( 'Number of Confs Loaded: ' + str(nc.getNumConfs()) )
# O of Conformations
print('Optimizing...')
_t1b = tm.time()
F = nc.optimizeGeomBFGS(conv=0.000001)
print('Optimization complete. Time: ' + "{:.4f}".format((tm.time() - _t1b) * 1000.0) + 'ms')
# Import pyNeuroChem import pyNeuroChem as pync import numpy as np import graphtools as gt # Set required files for pyNeuroChem wkdir = '/home/jujuman/Dropbox/ChemSciencePaper.AER/ANI-1-ntwk/' cnstfile = wkdir + 'rHCNO-4.6A_32-3.1A_a8-8.params' saefile = wkdir + 'sae_6-31gd.dat' nnfdir = wkdir + 'networks/' #dtdir = '/home/jujuman/Research/GDB-11-wB97X-6-31gd/dnntsgdb11_01/data/' #xyz,typ,Eact,tmp = gt.readncdat(dtdir + 'gdb11_s01-1_test.dat',np.float32) file = '/home/jujuman/Research/GDB-9-C7O2H_isomers/dsgdb9nsd_080323.xyz' xyz,typ,Na = gt.readxyz(file) # Construct pyNeuroChem class nc = pync.pyNeuroChem(cnstfile, saefile, nnfdir, 0) # Set the conformers in NeuroChem nc.setMolecule(coords=xyz[0],types=typ) #nc.setMolecule(coords=xyz,types=typ) # Print some data from the NeuroChem print( 'Number of Atoms Loaded: ' + str(nc.getNumAtoms()) ) print( 'Number of Confs Loaded: ' + str(nc.getNumConfs()) ) O = nc.optimize(conv=0.000001) print(O)
