def __update_many_mol2(inp, suffix, wfn_suffix, g09_suffix, input_type, charges):
"""
updates many mol2 files at the same time
"""
from a2mdio.qm import WaveFunction, GaussianLog
from a2mdio.molecules import UNITS_TABLE
if input_type == 'json':
with open(inp) as f:
input_contents = json.load(f)
elif input_type == 'csv':
with open(inp) as f:
input_contents = [i.strip() for i in f.readlines()]
else:
print("unknown format. use either csv or json")
sys.exit()
for name in input_contents:
mm = Mol2(name + '.mol2')
wfn = name + wfn_suffix
gaussian_log = name + g09_suffix
wfn_instance = WaveFunction(file=wfn, prefetch_dm=False, verbose=False)
glog = GaussianLog(file=gaussian_log, method='', charges=charges, verbose=False)
gdict = glog.read()
mm.coordinates = wfn_instance.get_coordinates() * UNITS_TABLE['au']['angstrom']
mm.charges = np.array(gdict['charges'], dtype='float64')
mm.write(name + suffix)
def __getitem__(self, item):
wfn = WaveFunction(file=self.idx[item], verbose=False)
centers = wfn.cent.tolist()
sym = wfn.sym.tolist()
exp = wfn.exp.tolist()
r = torch.tensor(wfn.get_coordinates(), dtype=torch.float)
dm = torch.tensor(wfn.density_matrix, dtype=torch.float)
return r, centers, exp, sym, dm
def __init__(self,
file,
verbose=False,
prefetch_dm=False,
batch_size=10000):
WaveFunction.__init__(self,
file=file,
verbose=verbose,
prefetch_dm=True,
batch_size=batch_size)
if prefetch_dm:
self.calculate_density_matrix()
def admin_sources(mm, reference, reference_type):
if reference_type == 'wfn':
reference_d = WaveFunction(verbose=False,
file=reference,
batch_size=10000)
elif reference_type == 'a2md':
reference_d = a2md_from_mol(mm)
with open(reference) as f:
reference_d.read(json.load(f))
else:
logger.error("use either wfn or a2md as reference format")
sys.exit()
return reference_d
def __update_mol2(name, wfn, gaussian_log, output, charges):
"""
updates a mol2 file using npa charges from gaussian output and coordinates of a wfn
"""
from a2mdio.qm import WaveFunction, GaussianLog
from a2mdio.molecules import UNITS_TABLE
mm = Mol2(name)
wfn_instance = WaveFunction(file=wfn, prefetch_dm=False, verbose=False)
glog = GaussianLog(file=gaussian_log, method='', charges=charges, verbose=False)
gdict = glog.read()
mm.coordinates = wfn_instance.get_coordinates() * UNITS_TABLE['au']['angstrom']
mm.charges = np.array(gdict['charges'], dtype='float64')
mm.write(output)
def __store_wfn(name, out, save_dm, save_coeff, program):
wfn = WaveFunction.from_file(name, program=program)
f = WaveFunctionHDF5(out, mode='w-')
f.add(name.replace('.g09', ''),
wfn,
save_dm=save_dm,
save_coeff=save_coeff)
f.close()
def dx_add_wfn_charge(name, dx, charge, output):
wfn = WaveFunction(file=name, verbose=False, batch_size=1000000)
convert2au = lambda x: x*UNITS_TABLE['angstrom']['au']
r3 = UNITS_TABLE['angstrom']['au'] ** 3
fun = lambda x : -wfn.eval(convert2au(x))*r3
dx1 = Volume(filename=dx)
dx1.read()
dx1.eval(fun)
dx2 = Volume(filename=dx)
dx2.read()
q = dx2._Volume__dx.sum() + charge
qt = dx1._Volume__dx.sum() * (dx1.get_basis()[0, 0] ** 3)
dx1._Volume__dx = dx1._Volume__dx * (q/ qt)
dx1._Volume__dx = -dx1._Volume__dx + dx2._Volume__dx
dx1.write(output)
return
def admin_sources(mm, reference, reference_type):
if reference_type == 'wfn':
reference_d = WaveFunction.from_file(filename=reference,
program='g09',
prefetch_dm=True)
elif reference_type == 'a2md':
reference_d = a2md_from_mol(mm)
with open(reference) as f:
reference_d.read(json.load(f))
else:
logger.error("use either wfn or a2md as reference format")
sys.exit()
return reference_d
def __many_store_wfn(name, out, save_dm, save_coeff, program):
with open(name) as f:
contents = [i.strip() for i in f.readlines()]
g = WaveFunctionHDF5(out, mode='w-')
for wfn_name in contents:
print(".. {:s}".format(wfn_name))
wfn = WaveFunction.from_file(wfn_name, program=program)
g.add(wfn_name.replace('.wfn', ''),
wfn,
save_dm=save_dm,
save_coeff=save_coeff)
f.close()
def __update_many_mol2(inp, suffix, wfn_suffix, g09_suffix, input_type,
charges):
"""
updates many mol2 files at the same time
"""
from a2mdio.qm import WaveFunction, GaussianLog
from a2mdio.molecules import UNITS_TABLE
if input_type == 'json':
with open(inp) as f:
input_contents = json.load(f)
elif input_type == 'txt':
with open(inp) as f:
input_contents = [i.strip() for i in f.readlines()]
else:
print("unknown format. use either csv or json")
sys.exit()
for i, name in enumerate(input_contents):
mm = Mol2(name + '.mol2')
wfn = name + wfn_suffix
gaussian_log = name + g09_suffix
wfn_instance = WaveFunction.from_file(filename=wfn,
program='g09',
prefetch_dm=False)
glog = GaussianLog(file=gaussian_log,
method='',
charges=charges,
verbose=False)
mm.coordinates = wfn_instance.get_coordinates(
) * UNITS_TABLE['au']['angstrom']
try:
gdict = glog.read()
mm.charges = np.array(gdict['charges'], dtype='float64')
except RuntimeError:
print('error : cant read file {:s}'.format(name + g09_suffix))
print('-- skipping charges for {:s}'.format(name + '.mol2'))
mm.write(name + suffix)
import torch
import time
import os
from a2mdnet.modules import QMDensityFun
from a2mdio.qm import WaveFunction, WaveFunctionHDF5
from a2mdtest.a2mdtests import methane, benzene
if __name__ == '__main__':
print("---")
print("-- qm density fun test")
device = torch.device('cuda:0')
start = time.time()
benzene_wfn = WaveFunction.from_file(benzene.wfn, program='g09')
methane_wfn = WaveFunction.from_file(methane.wfn, program='g09')
wfnh5 = WaveFunctionHDF5('.wfn.h5py', mode='w')
wfnh5.add(key='benzene', wfn=benzene_wfn)
wfnh5.add(key='methane', wfn=methane_wfn)
wfnh5.close()
end = time.time()
print("-- {:12.4f}".format(end - start))
print("-- done!")
load_qm = lambda cwfn: QMDensityFun(
group=cwfn, dtype=torch.float, device=device)
wfnh5 = WaveFunctionHDF5('.wfn.h5py', mode='r', wfn_init=load_qm)
for _, torch_wfn in wfnh5.iterall():
for i in range(10):
start = time.time()
from a2mdio.qm import GaussianLog
from a2mdio.parsers import forces
from a2mdtest.a2mdtests import aca
from a2mdio.qm import WaveFunction
from a2mdtest.a2mdtests import ammonium
from a2mdio.wfx import WaveFunctionX
from a2mdio.utils import eval_volume
import numpy as np
if __name__ == '__main__':
sample = np.loadtxt(ammonium.surfaces[0], delimiter=',', skiprows=1)
r = sample[:, :3]
p = sample[:, 3]
wfn = WaveFunction.from_file(ammonium.wfn, program='g09', prefetch_dm=True)
pr = wfn.eval(r)
l2 = ((p - pr)**2).sum()
print("-- l2 = {:6.4f}".format(l2))
print("done!")
# gl = GaussianLog(
# file='urea_c_000968.g09.output', method='dft-B3LYP',
# charges='MK', ep=False
# )
# c, f = gl.seek(forces)
# for (x, y, z) in f:
# print("{:8.4f} {:8.4f} {:8.4f}".format(x, y, z))
# print("DONE!")
# out_dict = gl.read()
#
# gl = GaussianLog(
# file=aca.out, method='MP2',
# charges='NPA', ep=False
from a2md.integrate import integrate_density_functional_gradient, dkl_gradient_functional, kullback_leibler_functional
from a2md.integrate import integrate_density_functional
from a2md.models import a2md_from_mol
from a2md.utils import RBFSymmetryCluster
from a2mdio.molecules import Mol2
from a2mdio.qm import WaveFunction
from a2mdtest.a2mdtests import water
from a2md.utils import project
from scipy.optimize import minimize
if __name__ == '__main__':
water_mol2 = Mol2(water.mol2)
water_a2md = a2md_from_mol(water_mol2)
water_wfn = WaveFunction(file=water.wfn)
water_density_sample = np.loadtxt(water.surfaces[1], skiprows=1, delimiter=',')
cm = RBFSymmetryCluster(verbose=False)
water_a2md.parametrize()
water_a2md.clustering(cm.cluster)
water_a2md.optimize(
training_coordinates=water_density_sample[:, :3],
training_density=water_density_sample[:, 3],
optimization_mode='restricted'
)
n = water_a2md.get_number_optimizable_functions()
x = water_a2md.get_unfrozen_integrals()
q = np.array(water_a2md.atom_charges).sum() - water_a2md.get_frozen_integrals().sum()
for fx in split_space(water_molecule, fun):
integral += pi_lebedev(
fun=fx,
r_max=15.0,
radial_res=100,
grid='tight'
)
print(integral)
print("done")
print("TE = {:8.4f}".format(time.time() - START))
START = time.time()
water_molecule = Mol2(water.mol2)
water_wfn = WaveFunction(file=water.path / "gdb_000003_sto3g.wfn", batch_size=20000)
fun = lambda x: water_wfn.eval(x)
integral = 0
for fx in split_space(water_molecule, fun):
integral += pi_lebedev(
fun=fx,
r_max=15.0,
radial_res=100,
grid='medium'
)
print(integral)
print("done")
print("TE = {:8.4f}".format(time.time() - START))