<s>
Newton-X	B-Application
is	O
a	O
general	O
program	O
for	O
molecular	O
dynamics	O
simulations	O
beyond	O
the	O
Born-Oppenheimer	O
approximation	O
.	O
</s>
<s>
Newton-X	B-Application
uses	O
the	O
trajectory	O
surface	B-Algorithm
hopping	I-Algorithm
method	O
,	O
a	O
semi-classical	O
approximation	O
in	O
which	O
the	O
nuclei	O
are	O
treated	O
classically	O
by	O
Newtonian	O
dynamics	O
,	O
while	O
the	O
electrons	O
are	O
treated	O
as	O
a	O
quantum	O
subsystem	O
via	O
a	O
local	O
approximation	O
of	O
the	O
Time-dependent	O
Schrödinger	O
Equation	O
.	O
</s>
<s>
Newton-X	B-Application
is	O
designed	O
as	O
a	O
platform	O
to	O
perform	O
all	O
steps	O
of	O
the	O
nonadiabatic	O
dynamics	O
simulations	O
,	O
from	O
the	O
initial	O
conditions	O
generation	O
,	O
through	O
trajectories	O
computation	O
,	O
to	O
the	O
statistical	O
analysis	O
of	O
the	O
results	O
.	O
</s>
<s>
It	O
works	O
interfaced	O
to	O
a	O
number	O
of	O
electronic	B-Application
structure	I-Application
programs	I-Application
available	O
for	O
computational	O
chemistry	O
,	O
including	O
Gaussian	B-Application
,	O
Turbomole	B-Application
,	O
Gamess	B-Application
,	O
and	O
Columbus	B-Application
.	O
</s>
<s>
Nonadiabatic	O
couplings	O
,	O
the	O
central	O
quantity	O
in	O
nonadiabatic	O
simulations	O
,	O
can	O
be	O
either	O
provided	O
by	O
a	O
third-party	B-Application
program	I-Application
or	O
computed	O
by	O
Newton-X	B-Application
.	O
</s>
<s>
When	O
computed	O
by	O
Newton-X	B-Application
,	O
it	O
is	O
done	O
with	O
a	O
numerical	O
approximation	O
based	O
on	O
overlap	O
of	O
electronic	O
wavefunctions	O
obtained	O
in	O
sequential	O
time	O
steps	O
.	O
</s>
<s>
Hybrid	O
combination	O
of	O
methods	O
is	O
possible	O
in	O
Newton-X	B-Application
.	O
</s>
<s>
These	O
hybrid	O
forces	O
may	O
,	O
for	O
instance	O
,	O
be	O
combined	O
into	O
the	O
popular	O
electrostatic-embedding	O
quantum-mechanical/molecular	O
-mechanical	O
method	O
(	O
QM/MM	B-Algorithm
)	O
.	O
</s>
<s>
Important	O
options	O
for	O
QM/MM	B-Algorithm
simulations	I-Algorithm
,	O
such	O
as	O
link	O
atoms	O
,	O
boundaries	O
,	O
and	O
thermostats	O
are	O
available	O
as	O
well	O
.	O
</s>
<s>
As	O
part	O
of	O
the	O
initial	O
conditions	O
module	O
,	O
Newton-X	B-Application
can	O
simulate	O
absorption	O
,	O
emission	O
,	O
and	O
photoelectron	O
spectra	O
,	O
using	O
the	O
Nuclear	O
Ensemble	O
approach	O
,	O
which	O
provides	O
full	O
spectral	O
widths	O
and	O
absolute	O
intensities	O
.	O
</s>
<s>
Newton-X	B-Application
can	O
simulate	O
surface-hopping	B-Algorithm
dynamics	I-Algorithm
with	O
the	O
following	O
programs	O
and	O
quantum-chemical	O
methods	O
:	O
</s>
<s>
The	O
surface	B-Algorithm
hopping	I-Algorithm
probability	I-Algorithm
depends	O
on	O
the	O
values	O
of	O
the	O
nonadiabatic	O
couplings	O
between	O
electronic	O
states	O
.	O
</s>
<s>
Newton-X	B-Application
can	O
either	O
compute	O
nonadiabatic	O
couplings	O
during	O
the	O
dynamics	O
or	O
read	O
them	O
from	O
an	O
interfaced	O
third-party	B-Application
program	I-Application
.	O
</s>
<s>
The	O
computation	O
of	O
the	O
couplings	O
in	O
Newton-X	B-Application
is	O
done	O
by	O
finite	O
differences	O
,	O
following	O
the	O
Hammes-Schiffer-Tully	O
approach	O
.	O
</s>
<s>
In	O
Newton-X	B-Application
,	O
it	O
is	O
used	O
with	O
a	O
number	O
of	O
quantum-chemical	O
methods	O
,	O
including	O
MCSCF	O
(	O
Multiconfigurational	O
Self-Consistent	O
Field	O
)	O
,	O
MRCI	O
(	O
Multi-Reference	O
Configuration	O
Interaction	O
)	O
,	O
CC2	O
(	O
Coupled	O
Cluster	O
to	O
Approximated	O
Second	O
Order	O
)	O
,	O
ADC(2 )	O
(	O
Algebraic	O
Diagrammatic	O
Construction	O
to	O
Second	O
Order	O
)	O
,	O
TDDFT	O
(	O
Time-Dependent	O
Density	O
Functional	O
Theory	O
)	O
,	O
and	O
TDA	O
(	O
Tamm-Dankov	O
Approximation	O
)	O
.	O
</s>
<s>
Newton-X	B-Application
simulates	O
absorption	O
and	O
emission	O
spectra	O
using	O
the	O
Nuclear	O
Ensemble	O
approach	O
.	O
</s>
<s>
where	O
e	O
is	O
the	O
elementary	O
charge	O
,	O
ħ	O
is	O
the	O
reduced	O
Planck	O
constant	O
,	O
m	O
is	O
the	O
electron	O
mass	O
,	O
c	B-Language
is	O
the	O
speed	O
of	O
light	O
,	O
0	O
is	O
the	O
vacuum	O
permittivity	O
,	O
and	O
nr	O
is	O
the	O
refractive	O
index	O
of	O
the	O
medium	O
.	O
</s>
<s>
The	O
development	O
of	O
Newton-X	B-Application
started	O
in	O
2005	O
at	O
the	O
Institute	O
for	O
the	O
Theoretical	O
Chemistry	O
of	O
the	O
University	O
of	O
Vienna	O
.	O
</s>
<s>
A	O
modulus	O
for	O
QM/MM	B-Algorithm
dynamics	O
was	O
developed	O
by	O
Matthias	O
Ruckenbauer	O
.	O
</s>
<s>
An	O
interface	O
to	O
Gamess	B-Application
was	O
added	O
by	O
Aaron	O
West	O
and	O
Theresa	O
Windus	O
(	O
Iowa	O
State	O
University	O
)	O
.	O
</s>
<s>
Mario	O
Barbatti	O
coordinates	O
new	O
program	O
developments	O
,	O
their	O
integration	O
into	O
the	O
official	O
version	O
,	O
and	O
the	O
Newton-X	B-Application
distribution	O
.	O
</s>
<s>
Newton-X	B-Application
is	O
distributed	O
free	O
of	O
charges	O
for	O
academic	O
usage	O
and	O
with	O
open	O
source	O
.	O
</s>
<s>
The	O
original	O
paper	O
describing	O
the	O
program	O
had	O
been	O
cited	O
190	O
times	O
by	O
December	O
22	O
,	O
2014	O
,	O
according	O
to	O
Google	B-Library
Scholar	I-Library
.	O
</s>
<s>
Newton-X	B-Application
counts	O
with	O
a	O
and	O
a	O
.	O
</s>
<s>
The	O
program	O
itself	O
is	O
distributed	O
with	O
a	O
collection	O
of	O
input	B-General_Concept
and	I-General_Concept
output	I-General_Concept
files	O
of	O
several	O
worked-out	O
examples	O
.	O
</s>
<s>
A	O
number	O
of	O
workshops	O
on	O
nonadiabatic	O
simulations	O
using	O
Newton-X	B-Application
have	O
been	O
organized	O
in	O
Vienna	O
(	O
2008	O
)	O
,	O
Rio	O
de	O
Janeiro	O
(	O
2009	O
)	O
,	O
Sao	O
Carlos	O
(	O
2011	O
)	O
,	O
Chiang	O
Mai	O
(	O
2011	O
,	O
2015	O
)	O
,	O
and	O
Jeddah	O
(	O
2014	O
)	O
.	O
</s>
<s>
A	O
main	O
concept	O
guiding	O
the	O
Newton-X	B-Application
development	O
is	O
that	O
the	O
program	O
should	O
be	O
simple	O
to	O
use	O
,	O
but	O
still	O
providing	O
as	O
many	O
options	O
as	O
possible	O
to	O
customize	O
the	O
jobs	O
.	O
</s>
<s>
Newton-X	B-Application
is	O
written	O
as	O
a	O
combination	O
of	O
independent	O
programs	O
.	O
</s>
<s>
The	O
coordinated	O
execution	O
of	O
these	O
programs	O
is	O
done	O
by	O
drivers	O
written	O
in	O
Perl	B-Language
,	O
while	O
the	O
programs	O
dealing	O
with	O
integration	O
of	O
the	O
dynamics	O
and	O
other	O
mathematical	O
aspects	O
are	O
written	O
in	O
Fortran	O
90	O
and	O
C	B-Language
.	O
Memory	O
is	O
dynamically	B-Application
allocated	I-Application
and	O
there	O
are	O
no	O
formal	O
limits	O
for	O
most	O
of	O
variables	O
,	O
such	O
as	O
number	O
of	O
atoms	O
or	O
states	O
.	O
</s>
<s>
Newton-X	B-Application
works	O
in	O
a	O
three-level	O
parallelization	B-Operating_System
:	O
the	O
first	O
level	O
is	O
a	O
trivial	O
parallelization	B-Operating_System
given	O
by	O
the	O
Independent-Trajectories	O
approach	O
used	O
by	O
the	O
program	O
.	O
</s>
<s>
In	O
a	O
second	O
level	O
,	O
Newton-X	B-Application
takes	O
advantage	O
of	O
the	O
parallelization	B-Operating_System
of	O
the	O
third-party	O
programs	O
with	O
which	O
it	O
is	O
interfaced	O
.	O
</s>
<s>
Thus	O
,	O
a	O
Newton-X	B-Application
simulation	O
using	O
the	O
interface	O
with	O
Gaussian	B-Application
program	O
can	O
be	O
first	O
distributed	O
over	O
a	O
cluster	O
in	O
terms	O
of	O
independent	O
trajectories	O
and	O
each	O
trajectory	O
runs	O
parallelized	B-Operating_System
version	O
of	O
Gaussian	B-Application
.	O
</s>
<s>
In	O
the	O
third	O
level	O
,	O
the	O
coupling	O
computations	O
in	O
Newton-X	B-Application
are	O
parallelized	B-Operating_System
.	O
</s>
<s>
Starting	O
with	O
version	O
(	O
1.3	O
,	O
2013	O
)	O
,	O
Newton-X	B-Application
uses	O
meta-codes	O
to	O
control	O
the	O
dynamics	O
simulation	O
behavior	O
.	O
</s>
<s>
To	O
keep	O
a	O
modular	O
architecture	O
for	O
easy	O
inclusion	O
of	O
new	O
algorithms	O
,	O
Newton-X	B-Application
is	O
organized	O
as	O
a	O
series	O
of	O
independent	O
programs	O
connected	O
by	O
general	O
program	O
drivers	O
.	O
</s>
<s>
For	O
this	O
reason	O
,	O
a	O
large	O
amount	O
of	O
input/output	B-General_Concept
is	O
required	O
during	O
the	O
program	O
's	O
execution	O
,	O
reducing	O
its	O
efficiency	O
.	O
</s>
<s>
Low	O
efficiency	O
due	O
to	O
input/output	B-General_Concept
can	O
,	O
however	O
,	O
be	O
relevant	O
with	O
semiempirical	O
methods	O
.	O
</s>
<s>
Other	O
problems	O
with	O
the	O
current	O
implementation	O
are	O
the	O
lack	O
of	O
parallelization	B-Operating_System
of	O
the	O
code	O
,	O
especially	O
of	O
the	O
couplings	O
computation	O
,	O
and	O
the	O
restriction	O
of	O
the	O
program	O
to	O
Linux	O
systems	O
.	O
</s>
