THE JOURNAL OF CHEMICAL PHYSICS 122, 124508 共2005兲

Geometry optimization of periodic systems using internal coordinates

Tomáš Bučkoa兲 and Jürgen Hafner
Computational Materials Science, Institut für Materialphysik, Universität Wien, Sensengasse 8/12,
A-1090 Wien, Austria
János G. Ángyánb兲
Laboratoire de Cristallographie et de Modélisation des Matériaux Minéraux et Biologiques, UMR 7036,
CNRS-Université Henri Poincaré, Boite Postale 239, F-54506 Vandœuvre-lès-Nancy, France
共Received 16 November 2004; accepted 11 January 2005; published online 30 March 2005兲

An algorithm is proposed for the structural optimization of periodic systems in internal 共chemical兲
coordinates. Internal coordinates may include in addition to the usual bond lengths, bond angles,
out-of-plane and dihedral angles, various “lattice internal coordinates” such as cell edge lengths, cell
angles, cell volume, etc. The coordinate transformations between Cartesian 共or fractional兲 and
internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the
previous formulation by Kudin et al. 关J. Chem. Phys. 114, 2919 共2001兲兴 includes the explicit
dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the
method, including constrained optimizations, is demonstrated on several examples, such as layered
and microporous materials 共gibbsite and chabazite兲 as well as the urea molecular crystal. The
calculations used energies and forces from the ab initio density functional theory plane wave
method in the projector-augmented wave formalism. © 2005 American Institute of Physics.
关DOI: 10.1063/1.1864932兴

I. INTRODUCTION vergence. Another approach is based on the construction of a

Recently, there has been an increasing interest in elec-
tronic structure calculations of three-dimensional periodic
systems. Several high-performance density functional theory
共Refs. 1–5兲 and Hartree–Fock5,6 codes are available, permit-
ting the study of structural features by gradient optimization.
Until very recently, geometry relaxations in solids were done
exclusively in terms of Cartesian and/or fractional coordi-
nates, and lattice vector components.1,4,7–9 Although the
Cartesian/fractional coordinates are simple and universally
applicable, the use of internal 共atomic and lattice兲 coordi-
nates as control parameters in geometry optimizations offer
several advantages. As it has been extensively demonstrated
for molecular examples,10–12 in internal coordinates 共i兲 it is
easy to have a good initial Hessian matrix guess, 共ii兲 the
coupling of different modes is reduced in comparison with
the Cartesian coordinates, and 共iii兲 the handling of con-
straints is simple and straightforward.
Inspired by the experience in the domain of finite mo-
lecular systems, several groups have attempted to improve
the convergence of geometry optimization of solids by
adopting alternative coordinate systems. Approximate nor-
mal mode coordinates derived from a simple model of the
dynamical matrix were proposed by Fernández-Serra et al.13
A scaling of these coordinates by estimated force constants
considerably improves the condition number 共ratio of highest
and lowest eigenvalue兲 of the Hessian and accelerates con-
a兲
Electronic mail: tomas.bucko@univie.ac.at
b兲
Electronic mail: janos.angyan@lcm3b.uhp-nancy.fr
redundant set of primitive internal coordinates, such as bond
lengths, valence angles, torsional angles, etc., that are trans-
lationally unique. Solid optimizations can be either per-
formed in these redundant coordinates directly14 or in a non-
redundant linear combination of them, in delocalized internal
coordinates.15 To our knowledge, the problem of lattice vec-
tor optimizations in the context of internal coordinates has
been discussed only in Ref. 14.
In the present work we describe an approach that uses
delocalized internal coordinates for the optimization of
atomic positions, similar to Ref. 15. The lattice parameter
optimization follows the principles of the Kudin’s method,14
with one significant improvement: while in their procedure
cell parameter variations are described by a small subset of
primitive internal coordinates, our method treats all atoms of
the unit cell on an equal footing letting them contribute to
cell parameter variations.
In Sec. II, after a short reminder of the Wilson B-matrix
formalism16 for geometry optimizations in internal coordi-
nates, the necessary extensions for the periodic case are dis-
cussed along with the handling of constraints. Some results
are presented in Sec. III, demonstrating that our procedure
allows one to optimize efficiently atomic coordinates and
cell parameters simultaneously. The gain in the number of
iterations for structures relaxed to a comparable degree of
precision with respect to Cartesian relaxations with a unit
Hessian matrix guess ranges from a factor of 2 to 10. In
addition to the better convergence properties, our approach
offers a significantly increased versatility in performing con-
strained lattice optimizations.

0021-9606/2005/122共12兲/124508/10/$22.50 122, 124508-1 © 2005 American Institute of Physics

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124508-2 Bučko, Hafner, and Ángyán J. Chem. Phys. 122, 124508 共2005兲

II. METHOD 1 dE
␴␣␤ = − 共6兲
A. Cartesian and fractional coordinates ⍀ d␧␣␤
The structure of a periodic system is characterized by by the relationship 共cf. the Appendix兲
three lattice vectors, arranged in the matrix h = 关a1 , a2 , a3兴
dE
and by the 3N fractional coordinates, s = 兵s␣a 其. The Cartesian
dh␣␤
=−⍀ 兺␥ ␴␣␥共ht兲␥␤
−1
. 共7兲
positions of atom a in the L = 共l1 , l2 , l3兲 unit cell of the solid
is given by the linear transformation Electronic structure codes usually provide Cartesian force
3 components, which can be transformed to fractional coordi-
r␣a,La = 兺
␤=1
h␣␤共s␤a + l␤a 兲. 共1兲 nate forces as
dE ⳵E ⳵ra ⳵E ⳵
The three lattice vectors form, in the general case, an unnor- ds␣a
= 兺␤ ⳵ra ⳵sa␤ = 兺␤ 兺␥ ⳵ra ⳵sa h␤␥共s␥a + l␥a 兲
␤ ␣ ␤ ␣
malized and nonorthogonal basis. The fractional coordinates
can be obtained from the Cartesian ones by the inverse trans- ⳵E
formation in terms of the reciprocal lattice vectors, 共ht兲−1 = 兺␤ ⳵ra h␤␣ . 共8兲
␤
= 关a*1 , a*2 , a*3兴, defined by a*i · a j = ␦ij as

冉兺␤ h␣␤−1 r␤a,L ,l␣a 冊 .

It should be noted that in addition to the explicit lattice vec-
s␣a = mod a 共2兲 tor dependence of the total energy, atomic forces contribute
also to the strain-derivative tensor, according to the follow-
The structural deformations in periodic systems arise from ing expression:
the change of atomic positions at constant lattice vectors on dE ⳵E ⳵E ⳵ra ⳵E ⳵E
the one hand, and from the deformation of the lattice vectors =
dh␣␤ ⳵h␣␤
+ 兺a ⳵ra ⳵h␣␤␣ = ⳵h␣␤ + 兺a ⳵ra s␤a . 共9兲
at constant fractional coordinates. The variation of lattice ␣ ␣

vectors is conveniently described by the strain tensor ␧␣␤ as As we shall see later, in Sec. II D, the same relationships can

兺␥ 共␦␣␥ + ␧␣␥兲h␥␤ .
be obtained directly from the B-matrix formalism, to be de-
⬘ =
h␣␤ 共3兲
veloped below.
The extended Hessian matrix F in Eq. 共5兲 is built up
Any change in h␣␤ implies a variation of atomic Cartesian from several blocks: that of the second derivatives of the
coordinates by Eq. 共1兲 which obey an analogous relationship energy with respect to atomic positions 共related to the dy-
namical matrix兲, that of the stress-strain derivatives, as well
r␣⬘ = 兺␤ 共␦␣␤ + ␧␣␤兲r␤ . 共4兲 as cross terms.

Out of the total number of 3N + 9 deformation variables 共3N

atomic coordinates and 9 strain tensor elements兲 the energy
is invariant with respect to six degrees of freedom: the posi-
tion of the origin and the orientation of the lattice vectors.
Although the origin of the lattice is arbitrary, it is usually
chosen on the basis of symmetry considerations. Overall ro-
tations of the lattice can be avoided by taking the symmetric
part of the strain tensor,17 or the metric matrix formed from
the six unique scalar products of lattice vectors,18 as inde-
pendent lattice variables.
Most of the geometry optimization algorithms are based
on a local harmonic expansion of the total energy around an
initial structure. Using exact first and approximate second
derivatives, a convenient step is predicted that takes the sys-
tem closer to the desired critical point 共minimum or saddle
point兲 with vanishing gradients. In periodic systems the sim-
plest coordinate system is constituted from the 3N fractional
atomic positions and nine lattice vector component varia-
tions, ␦x = 兵␦s , ␦h其 leading to the following expansion:
E共x + ␦x兲 − E共x兲 = − ft␦x + 21 ␦xtF␦x + ¯ + . 共5兲
The elements of the column vector f are either the forces,
f ␣a = −dE / ds␣a , or the lattice vector derivatives of the total
energy, f ␣␤ = −dE / dh␣␤. The latter are related to the stress
tensor elements, i.e., the negative volume-normalized strain
derivatives of the energy:
B. Curvilinear internal coordinates for periodic
systems
In contrast to the set of external coordinates, ␦x
= 兵␦s , ␦h其, including overall rotations and translations of the
system, one can define a set of internal coordinates, ␦␰
= 兵␦q , ␦q̂其, which involve only internal degrees of freedom.
Internal atomic coordinates, such as bond lengths, bond
angles, torsion angles, etc., or their linear combinations are,
in general, nonlinear functions of Cartesian coordinates, qi
= f共兵r␣a,La其兲, and by the virtue of the linear relationship Eq.
共1兲, also of the fractional coordinates and the lattice vectors.
Similarly, internal lattice coordinates, such as cell edge
length, cell angle, volume, etc., are determined by the three
lattice vectors, q̂i = f共兵h␣␤其兲.
Internal coordinate deformations are related to external
coordinate deformations by a nonlinear 共curvilinear兲 trans-
formation, usually approximated by a truncated Taylor ex-
pansion
⳵␰i 1 ⳵ 2␰ i
␦␰i = 兺 ␦xs + 兺 ␦ r s␦ r t + ¯
s ⳵xs 2 st ⳵xs⳵rt
= 共B␦x兲i + 21 ␦xtCi␦x + ¯ . 共10兲
Inserting expansion 共10兲 into the harmonic expansion of the
total energy with respect to internal coordinates

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124508-3 Geometry optimization of periodic systems
E共␰ + ␦␰兲 − E共␰兲 = − ␸t␦␰ + 21 ␦␰tH␦␰ + ¯ 共11兲
and equating terms of the same order, we obtain a relation-
ship between external and internal force/stress components
Bt␸ = f, 共12兲
while the external coordinate deformations can be obtained
from a set of internal distortions by the first-order relation-
ship
B␦x = ␦␰ . 共13兲
The matrix B is a generalization of Wilson’s B-matrix16 for
periodic systems. As in the molecular case, the number M of
internal coordinates that can be constructed for an N-atom
periodic structure is usually much more than the 3N + 3 geo-
metrical degrees of freedom. Since ␦x, f 苸 R3N+9 and ␦␰, ␸
苸 R M , B 苸 R M⫻3N+9, the B-matrix 共unless M = 3N + 3 and the
set of internal coordinates is nonredundant兲 and the solutions
of the above equations are given by the Moore–Penrose
pseudoinverses as
␸ = 共Bt兲+f, 共14兲
␦ x = B +␦ ␰ . 共15兲
The same B-matrix and its pseudoinverse appear in the trans-
formation of the fractional 共F兲 and internal 共H兲 second de-
rivative matrices
F ⬇ B HB,
t
共16兲
H ⬇ 共Bt兲+FB+ , 共17兲
where the correction term involving the second derivative of
the internal coordinates with respect to the fractional ones
has been neglected.12
In the case of really large systems 共⬎1000 atoms兲, the
coordinate and force transformation steps may become the
bottleneck of the optimization procedure. Various methods
have been proposed to solve efficiently the above equations
for extended systems.19–23 In the present implementation de-
localized internal coordinates15,21,24,25 are used, which are
particularly appropriate for medium-sized problems.
C. Delocalized internal coordinates
Even for small systems, the number of generated internal
coordinates is usually much larger than the number of ionic
degrees of freedom 共i.e., 3N − 6 for molecules and 3N + 3 for
systems with three-dimensional periodicity兲. The handling of
this set of redundant coordinates may lead to a significant
increase of the computational time and may cause conver-
gence problems in the coordinate back-transformation step.
To avoid these problems, Baker et al. proposed the use of
nonredundant linear combinations of primitive internal
coordinates.24 Taking the singular value decomposition of
the B-matrix, as B = UtBDV, where U and V are unitary ma-
trices and BD is a diagonal matrix formed from the eigenvec-
tors associated with the nonzero eigenvalues of 共BBt兲. After
multiplication of the B-matrix equation from left by U, one
obtains
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J. Chem. Phys. 122, 124508 共2005兲
BDVx = Uq, 共18兲
which can be considered as the defining relationship of the
delocalized internal coordinate transformation:
B̃x = q̃ 共19兲
with B̃ = BDV and q̃ = Uq. Note that B̃+, the pseudoinverse of
−1
B̃, is simply VtBD . The transformation relations Eqs.
共14兲–共17兲, for the primitive internal coordinates remain valid
for the delocalized internal coordinates after switching from
B to B̃.
D. B-matrix for periodic systems
The construction of the B-matrix for periodic systems,
defined by atomic position and lattice vector components,
needs some special consideration as compared to the mo-
lecular case. Kudin et al. remarked14 that primitive internal
coordinates involving atoms that belong to different unit
cells are explicitly dependent on the lattice vector compo-
nents h␣␤. They have written expression 共1兲 in the following
form:
r␣a,L = r␣a,0 + 兺␤ h␣␤l␤ , 共20兲
and generated the corresponding B-matrix elements by the
application of the chain rule. In their formulation only inter-
cell coordinates 共L ⫽ 0兲 are allowed to contribute to the lat-
tice B-matrix elements. The optimization of lattice param-
eters is treated in an indirect manner, through intercell
distances between atoms and their periodic images as well as
through angles between three replicates of the same atom
lying in different unit cells. This procedure seems to be well
adapted to simple molecular crystals, but it is much less con-
venient for ionic systems, oxides or atomic lattices, where
the distinction between intracell and intercell coordinates is
less obvious. In the following we propose a “democratic”
approach taking into consideration that any unique internal
coordinate deformation may influence the lattice parameters.
Let us consider the augmented B-matrix equation
冉 冊冉 冊冉 冊
␦q Bqs Bqh ␦s
= q̂s q̂h , 共21兲
␦q̂ B B ␦h
where the individual blocks Bqs and Bq̂s describe the linear
transformation of the atomic positions s␣a , while the blocks
Bqh and Bq̂h describe transformations involving the lattice
vector components h␣␤ to atomic qi and lattice internal q̂ j
coordinates. The blocks of the augmented B-matrix can be
calculated from the relationships 共1兲 and 共2兲 using the chain
rule.
An internal coordinate may depend on the Cartesian co-
ordinates of atoms in different unit cells. Therefore the
B-matrix elements between fractional atomic distortions and
unique internal coordinates should be calculated as
124508-4 Bučko, Hafner, and Ángyán J. Chem. Phys. 122, 124508 共2005兲

qs ⳵qi共r␣a,La,r␤b,Lb, . . . 兲 ␦r␣a,La = 兺 h␣␥␦s␥a + 兺 共s␤a + l␤a 兲␦h␣␤ , 共27兲

Bi,a = ␥ ␣␤
␣ ⳵s␣a
⳵q ⳵r␤a,La ⳵qi we retrieve the expected result that the variation of a Carte-
= 兺 兺 a,Li
L ␤ ⳵r
a ⳵sa
= 兺 兺 a,L h␤␣ .
La ␤ ⳵ r ␤
a
共22兲 sian coordinate can be decomposed into a variation of the
a ␤ ␣ fractional coordinate, ␦s␣a , and a variation of the lattice vec-
tor components, ␦h␣␤.
Disregarding the transformation from Cartesian to fractional
The transformation equations for the forces and stresses,
coordinates, the B-matrix elements for internal coordinates
Eq. 共12兲, lead to the following relationships 关cf. Eqs. 共8兲 and
that “remain” entirely in the unit cell are identical to those of
共9兲兴 between the energy derivatives with respect to fractional
a nonperiodical system. If several translated copies of the
coordinates, cell parameters, and Cartesian coordinates:
same atom participate in a given internal coordinate, the con-
dE ⳵E
兺␤ 共h␣␤兲t ⳵ra ,
tributions from different cells should be summed up. This
= 共28兲
leads to somewhat unexpected consequences. For instance, ds␣a ␤
in the case of a monoatomic lattice, a zero B-matrix element
is obtained with respect to the atomic position, reflecting the dE ⳵E ⳵E
fact that in this case the independent variable is the cell pa- =
dh␣␤ a,La
兺
共s␤a + l␤a 兲 a +
⳵r␣ ⳵h␣␤
. 共29兲
rameter itself.
The proportionality between an internal coordinate de- The first of these equations is a simple linear transformation
formation ␦qi and a lattice vector distortion ␦h␣␤ is described of the force components from a Cartesian to a lattice vector
by the following B-matrix elements: reference system. The second equation tells that the total
derivatives with respect to the lattice parameters have a con-
⳵qi共r␣a,La,r␤b,Lb, . . . 兲
Bi,qh␣␤ = tribution from the partial derivative of the energy with re-
⳵h␣␤ spect to the lattice parameters 共explicit dependence兲 and a
⳵q ⳵r␥a,La “virial contribution” proportional to the atomic force
= 兺 兺 a,Li
a,L ␥ ⳵r
a ⳵h
␣␤
components.26 The latter term, which obviously vanishes if
a ␥ the atomic forces are zero, is analogous to the expression of
⳵q the virial pressure discussed by several authors in a some-
= 兺 兺
a,L ␥ ⳵ r a,L ␦␣␥共s␤ + l␤兲
i a
a
a
what different context.27–29
a ␣

⳵q
= 兺 a,Li 共s␤a + l␤a 兲,
a,L ⳵r
a
共23兲 E. Constraints
a ␣
Constrained geometry optimizations are helpful and
where the superscript qh refers to the type of B-matrix ele- even necessary in most of the applications of ab initio cal-
ment. culations to chemical reactions, phase transitions, etc. The
The “lattice internal” coordinates q̂, such as cell edge general strategy is to make vanish, exactly or at least ap-
lengths, a / b ratio, cell angles, volume, etc., do not depend proximately, forces along the constrained coordinates to
explicitly on the fractional atomic positions, therefore the avoid deformations involving the variation of the constrained
block of the extended B-matrix is zero, Bq̂s = 0. The transfor- coordinates. The principal advantage of using internal coor-
mation between the lattice vector changes and various “in- dinates is that one can impose exact internal coordinate con-
ternal” lattice parameters is described by the matrix elements straints during the optimization. Various algorithms, such as
the use of projection operator,30 orthogonalization,24 and
⳵q̂i Lagrange multiplier31 techniques have been proposed in the
Bi,q̂h␣␤ = . 共24兲
⳵h␣␤ past. Our implementation follows essentially the orthogonal-
ization algorithm of Ref. 24.
For instance, the following relationship holds for q̂i = ⍀, the
In the first step, the B-matrix is modified in such a way
unit cell volume:
that first derivatives of the active coordinates 共those coordi-
nates which are allowed to be relaxed兲 are orthogonalized
␣␤ = ⍀共h 兲␣␤ . 共25兲
q̂h t −1
B⍀,
with respect to each constrained coordinate qc. The rows B j
Other specific lattice B-matrix elements can also be derived are modified according to the formula
from the definition of lattice vector lengths and lattice 共B j · Bc兲 Bc
angles. B̄ j = B j − 兺c 兩Bc兩 兩Bc兩
, 共30兲
In order to appreciate the role of the extended B-matrix
in lattice optimizations, let us consider the special case of where the summation is over the constrained coordinates. If
Cartesian coordinates as internals, i.e., ␦␰ = 兵␦r , ␦h其. Accord- one of the rows of the original B-matrix is identical to a
ing to the coordinate transformation relationship, Eq. 共13兲, constrained coordinate, it is exactly annihilated in this step.
Delocalized internal coordinates and corresponding gra-
␦r = Brs␦s + Brh␦h 共26兲
dients are generated from the modified matrix B̄, as de-
and using the matrix elements given by Eqs. 共22兲 and 共23兲, scribed in previous sections. The delocalized coordinates are

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124508-5 Geometry optimization of periodic systems
now linear combinations of either constrained, or active co-
ordinates, but not of both. Finally, the gradients for delocal-
ized coordinates corresponding to constrained coordinates
are set to zero. The optimization then proceeds as in the case
of an unconstrained relaxation. Not only single primitive in-
ternal coordinates but also the ratios and sums of primitive
internal coordinates, the norms of vectors whose components
are primitive internal coordinates 共e.g., vibrational modes兲,
lattice parameters, the volume of the unit cell and many other
coordinate types can be constrained. Note that Cartesian co-
ordinates can be taken as special 共single-body兲 primitive in-
ternal coordinates.
Special attention should be paid to the constrained opti-
mizations where the lattice parameters are allowed to
change, but some of the internal degrees of freedom are fro-
zen. The components of the Cartesian forces that correspond
to the fixed internal coordinates should be subtracted from
this expression of the stress tensor, in order to avoid their
“contamination.” Our B-matrix technique, if used consis-
tently, takes care of these effects.
F. Optimization strategy
The minimization algorithm used in this study is based
on the geometrical direct inversion in the iterative subspace
共DIIS兲 method by Császár and Pulay32 improved recently by
Farkas and Schlegel.33 In this method the information on the
potential energy surface collected in the preceding M relax-
ation steps is used to minimize the norm of the error vector
defined as a linear combination of gradients ˜␸ corresponding
to delocalized internal coordinates q̃,
k
rk = 兺
i=k−M
ci˜␸i .
The coefficients ci are obtained by minimizing 兩r兩2 under
the constraint 兺i=k−M
k
ci = 1 leading to a set of equations
冢 冣冢 冣 冢 冣
˜␸k−M
t
˜␸k−M . . . ˜␸k−M
t
˜␸k 1 ck−M
. ... . . . .
. ... . . . .
= .
. ... . . . .
˜␸tk˜␸k−M ... ˜␸tk˜␸k 1 ck
1 ... 1 0 ␭ 1
A new set of delocalized internal coordinates is calculated
using
M M
兺 兺
q̃k+1 = ciq̃i + H̃ −1
c i␸
˜ i.
i=k−M i=k−M
The dimension M of the iterative subspace used in DIIS
has substantial impact on efficiency of the relaxation. When
the structure is close to the minimum 共i.e., in the harmonic
region兲 M should be relatively high 共ten or more兲. When
starting from a poor guess and the landscape of the potential
energy is not well described by a harmonic approximation, a
better performance can be achieved by using only a limited
number of previous relaxation steps.
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J. Chem. Phys. 122, 124508 共2005兲
Farkas and Schleger33 suggested an improved DIIS algo-
rithm, which allows one to adjust automatically the dimen-
sion of the iterative subspace. The idea is that the ionic step
produced by DIIS ⌬q̃ = q̃k+1 − q̃k is compared to a simple
quasi-Newton step ⌬q̃QN = H̃−1˜␸ and should meet the follow-
ing criteria.
共i兲 The direction of the DIIS step ⌬q̃ deviates from ⌬q̃QN
by an angle ␾. The step is accepted if cos共␾兲 is larger than
0.97, 0.84, 0.71, 0.67, 0.62, 0.56, 0.49, and 0.41 for two to
nine recent relaxation steps used in DIIS. For a dimension of
ten or higher this criterion is not taken into account.
共ii兲 The norm of DIIS step is limited to be not more than
ten times larger than that of the reference step.
共iii兲 The sum of all positive coefficients ci should not
exceed the value of 15.
共iv兲 The magnitude of c / 兩r兩2 should not exceed 108.
If one of these criteria is not fulfilled, the step is not
accepted and the most remote vector is removed from the
iterative subspace. This procedure is repeated until all crite-
ria are fulfilled.
One of the major advantages of the use of internal in-
stead of Cartesian coordinates is that a reasonable guess for
Hessian matrix can be constructed. Even a very simple
model Hessian which is just a diagonal matrix with elements
0.5, 0.2, and 0.1 a.u. for bonds, angles, and torsions, respec-
tively, usually works very well. Lindh et al.34 proposed a
model Hessian, constructed from force constants that are
simple functions of nuclear positions
kij = kr␳ij , 共34兲
共31兲 kijk = k␾␳ij␳ jk , 共35兲
kijkl = k␶␳ij␳ jk␳kl , 共36兲
with
0
␳ij = exp关␣ij共r20,ij − r2ij兲兴. 共37兲
For the first three rows of the periodic table one needs alto-
gether 15 independent parameters for the quantities kr, k␾, k␶,
␣ij, and r0,ij that are collected in Table I. The model Hessian
0
can be easily transformed to delocalized internal coordinates
using the formula
共32兲
H̃ = UtHU. 共38兲
In the course of the relaxation, the Hessian matrix is
updated using the Broyden–Fletcher–Goldfarb–Shanno algo-
rithm:
冉 冊
共33兲
⌬˜␸k⌬˜␸tk H̃k−1⌬q̃k−1⌬q̃k−1
t
H̃k−1
H̃k = H̃k−1 − + , 共39兲
⌬˜␸k−1⌬q̃k
t
⌬q̃k−1
t
H̃k−1⌬q̃k−1
where ⌬˜␸k = ˜␸k − ˜␸k−1 is the change of gradients associated
with the the relaxation step ⌬q̃k = q̃k − q̃k−1.
The performance of our optimization engine GADGET is
checked against the “native” Vienna ab initio simulation
package 共VASP兲 optimizer using the conjugate gradient al-
gorithm and performed in cartesian coordinates. The conju-
124508-6 Bučko, Hafner, and Ángyán J. Chem. Phys. 122, 124508 共2005兲

TABLE I. Parameters of the model Hessian proposed by Lindh et al. 共Ref. 34兲. Indices i and j designate the
rows of the periodic table of elements to which the atoms correspond. The universal stretch, bend, and torsion
coefficients are kr = 0.45, k␾ = 0.15, and k␶ = 0.005. All quantities are given in atomic units.

First period Second period Third period

␣ij First period 1.0000 0.3949 0.3949

Second period 0.3949 0.2800 0.2800
Third period 0.3949 0.2800 0.2800

r0,ij First period 1.35 2.10 2.53

Second period 2.10 2.87 3.40
Third period 2.53 3.40 3.40

gate gradient algorithm tries to improve a simple steepest the plane wave basis-set incompleteness error.37 The applied
descent step 共i.e., in the direction of gradient兲 by conjugating cutoff energy of 800 eV is pretty high and it is usually as-
the search direction from the most recent step. It starts with sumed that in this case the Pulay stress is negligible. Some-
the steepest descent direction, but in all the following steps what unexpectedly, we have found relatively small but nev-
the search direction 共sk+1兲 is given by ertheless significant residual stresses at the equilibrium
volume obtained by fitting a Murnaghan equation of state to
fk + fk−1 · fk
␥= , 共40兲 a series of fixed-volume relaxed structures. This residual
fk−1 · fk−1 stress 共Pulay stress兲 can be added as a constant in the auto-
matic relaxation procedure, in order to correct the finite-basis
sk+1 = fk + ␥sk . 共41兲 error in the direct lattice optimizations.
The conjugate gradient algorithm requires the line mini- Different kinds of optimizations were performed, all
mization along search direction. starting from the same initial geometry. 共i兲 Only the atomic
positions are optimized at constant lattice parameters, using
delocalized internal coordinates 共GADGET兲. 共ii兲 Atomic posi-
III. APPLICATIONS tion relaxation with the native VASP optimizer. 共iii兲 Simul-
taneous atomic parameter and lattice parameter optimization
The electronic structure calculations were done with the
in delocalized internal coordinates with GADGET. 共iv兲 Full
VASP,1 using the density functional theory in the generalized
atomic position and lattice parameter relaxation with VASP.
gradient approximation. The PW91 exchange-correlation
共v兲 Multistep geometry relaxation with GADGET using a se-
functional was used, using the projector-augmented wave
ries of fixed-volume relaxations to determine a Murnaghan-
formalism.35,36 The calculations were done with high preci-
type equation of state 共EOS兲 and reoptimizing the structure
sion, i.e., the wave function was developed on a plane wave
at the volume of the interpolated minimum. 共vi兲 Full delo-
basis with a cutoff of 800 eV, and the support grid for the
calized internal coordinate relaxation using the Pulay stress
representation of the charge density was sufficiently precise
deduced from the EOS optimization.
to avoid any wraparound errors. The electronic wave func-
tions were converged in each step to 2.7⫻ 10−8 hartree. It is
expected that these computational parameters allow us to A. Microporous material: SiO2 chabazite
obtain quite reliable forces. Chabazite 共Fig. 1兲 is microporous aluminosilicate min-
The geometry optimizations were done with the external eral 共zeolite兲 in which every Si 共Al兲 atom is coordinated by
optimizer GADGET, written in Python. GADGET reads the ge- four O atoms. The space groups of the purely siliceous cha-
ometry, energy, and gradients from the VASP output, sets up
internal coordinates, estimates an optimal move, calculates
the new set of lattice parameters and Cartesian coordinates,
and starts a new VASP calculation, until convergence. As we
shall see, the additional overhead related to the repeated re-
starts of VASP is largely compensated by the gain in the
number of iterations. Our optimizer can be easily interfaced
with other packages that calculate total energies and forces/
stresses, and such an interface is already operational with the
5
GAUSSIAN 03 package. Optimizations were carried out using
the geometrical DIIS method with an iterative subspace of
dimension 5. Convergence criteria involve the simultaneous
fulfillment of an energy change less than 1 ⫻ 10−6 a.u., a
maximal gradient less than 2 ⫻ 10−4 a.u., and a volume
change 共in lattice relaxations兲 that is smaller than 0.05%.
In lattice parameter optimizations, involving volume
changes, we are faced with the problem of “Pulay stress,” i.e. FIG. 1. Rhombohedral unit cell of purely siliceous chabazite, Si12O24.

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124508-7 Geometry optimization of periodic systems J. Chem. Phys. 122, 124508 共2005兲

TABLE II. Optimization of the chabazite structure: the initial configuration 共Initial兲; relaxation of the ionic degrees of freedom using delocalized internal
coordinates 共兵q其兲 and using the VASP native optimizer 共兵s其兲; relaxation of the lattice parameters and ionic positions using delocalized internal coordinates
共兵q , q̂其兲 and with the VASP native optimizer 共兵s , h其兲; minimum of the fitted Murnaghan equation of state 共EOS兲; and the full relaxation using delocalized
internal coordinates with stress corrected for a Pulay stress 共兵q , q̂ ; ␴其兲. Listed are cell parameters 关a, b, c 共Å兲; ␣, ␤, ␥ 共deg.兲兴, energy 共hartree兲, gradient 共a.u.兲,
stress 共kB兲, cell volume 共Å3兲, and the number of relaxation steps.

Parameter Initial 兵q其 兵s其 兵q , q̂其 兵s , h其 EOS 兵q , q̂ ; ␴其

a 9.301共9兲 9.349共7兲 9.354共1兲 9.349共6兲 9.351共6兲

b 9.307共2兲 9.344共5兲 9.380共0兲 9.349共6兲 9.347共6兲
c 9.303共9兲 9.347共7兲 9.347共6兲 9.349共9兲 9.350共1兲
␣ 94.122共4兲 94.263共5兲 94.113共4兲 94.179共4兲 94.158共3兲
␤ 94.058共9兲 94.286共7兲 94.228共1兲 94.186共0兲 94.179共9兲
␥ 94.104共5兲 94.280共5兲 94.166共0兲 94.187共8兲 94.176共0兲
E −10.378 55 −10.535 66 −10.535 66 −10.537 09 −10.537 06 −10.537 11 −10.537 10
gmax 0.132 18 0.000 15 0.000 15 0.000 11 0.000 16 0.000 05 0.000 14
␴xx 36.30 9.74 9.49 0.00 0.10 −0.59 −0.59
␴yy 35.74 9.12 8.92 0.01 0.07 −0.59 −0.58
␴zz 17.15 9.37 9.19 0.00 0.07 −0.62 −0.62
␴xy 2.17 -0.31 -0.60 0.00 0.01 −0.09 −0.09
␴yz 24.34 −0.33 −0.59 −0.01 −0.02 −0.12 −0.13
␴zx 4.17 −0.41 −0.49 0.00 −0.03 −0.10 −0.10
⍀ 799.00 799.00 799.00 809.50 809.69 810.44 810.51
Nion 22 70 25 62 25

bazite is R3̄m 共No. 166兲, however, we have chosen a slightly
perturbed initial configuration, corresponding to a highly sili-
ceous protonated framework.38 The primitive unit cell con-
tains 12 Si 共Al兲 atoms and 24 O atoms giving a total of 288
primitive internal coordinates 共bonds, angles, and torsions兲.
The results obtained after various types of relaxations are
summarized in Table II. In every case our algorithm outper-
formed the native VASP optimizer by a factor of 2–3. The
minimum of the full relaxation is checked against a fit to the
Murnaghan equation. In spite of the high plane wave cutoff,
the effect of the Pulay stress is not negligible: the residual
stress was found to be around −0.6 kB. The cell volume for
the resulting configuration is by ⬃1 Å3 too low compared to
the true minimum.
The underestimation of the equilibrium cell volume due
to the Pulay stress is a quite general phenomenon observed
in all examples given here. The full relaxation with compen-
sation for a Pulay stress leads to the structure which is very
close to a minimum of the Murnaghan equation. The sym-
metry of the unit cell is not completely recovered 共a ⫽ b
⫽ c兲 in full relaxations, due to the fact that the lattice param-
eters are usually “softer” than the atomic degrees of freedom
and thus more difficult to relax. In order to relax to a true
symmetry, a more stringent relaxation criterion for the stress
tensor would be required.
retical vibrational spectrum of gibbsite and bayerite in light
of some new experimental results.42
In this system the conventional primitive internal coor-
dinates 共bonds, angles, and torsions兲 are insufficient to de-
scribe all atomic degrees of freedom. In order to describe
correctly the mutual position of subsequent layers we have
used inverse power distance coordinates 共5 / r coordinates兲
proposed by Baker and Pulay.43 The 5 / r coordinates were
generated only for pairs of atoms lying in different structural
fragments 共layers兲 and satisfying the condition that the cor-
responding interatomic distance is smaller than 1.6 times the
sum of the covalent radii. In this way we have generated 664
conventional primitive and 179 inverse-power distance coor-
dinates. Data for the initial configuration and for the relaxed
structures are collected in Table III. The performance of our
method is by a factor of 10 better than the conjugate gradient

B. Layered oxide: Gibbsite

Unlike chabazite, gibbsite 关Al共OH兲3兴 共see Fig. 2兲 is a
layered mineral.39 The individual layers are charge balanced
which results into very weak interlayer interactions. The
primitive cell of gibbsite is monoclinic with space group
symmetry P121 / n1 共No. 14兲. There has been several recent
ab initio structural studies on gibbsite and other Al共OH兲3
polymorphs40,41 and we are currently working on the theo- FIG. 2. Crystal structure of gibbsite, Al共OH兲3.

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124508-8 Bučko, Hafner, and Ángyán J. Chem. Phys. 122, 124508 共2005兲

TABLE III. Optimization of the gibbsite structure: the initial configuration 共Initial兲; relaxation of the ionic degrees of freedom using delocalized internal
coordinates 共兵q其兲 and using the VASP native optimizer 共兵s其兲; relaxation of the lattice parameters and ionic positions using delocalized internal coordinates
共兵q , q̂其兲 and with the VASP native optimizer 共兵s , h其兲; minimum of the fitted Murnaghan equation of state 共EOS兲; and the full relaxation using delocalized
internal coordinates with stress corrected for a Pulay stress 共兵q , q̂ ; ␴其兲. Listed are cell parameters 关a, b, c 共Å兲; ␣, ␤, ␥ 共deg.兲兴, energy 共hartree兲, gradient 共a.u.兲,
stress 共kB兲, cell volume 共Å3兲, and the number of relaxation steps.

Parameter Initial 兵q其 兵s其 兵q , q̂其 兵s , h其 EOS 兵q , q̂ ; ␴其

a 8.497共8兲 8.779共2兲 8.769共6兲 8.774共9兲 8.776共6兲

b 4.977共5兲 5.103共5兲 5.102共8兲 5.113共3兲 5.111共2兲
c 9.378共5兲 9.711共8兲 9.699共6兲 9.714共8兲 9.716共3兲
␣ 90.230共4兲 90.024共7兲 90.016共7兲 89.982共6兲 90.032共2兲
␤ 91.955共9兲 92.157共8兲 92.153共5兲 92.130共0兲 92.142共3兲
␥ 89.995共0兲 89.991共8兲 89.995共3兲 89.997共5兲 89.987共2兲
E −12.037 47 −12.038 57 −12.038 52 −12.065 39 −12.065 33 −12.065 42 −12.065 41
gmax 0.047 95 0.000 10 0.000 18 0.000 12 0.000 30 0.000 07 0.000 12
␴xx 62.48 64.80 64.64 0.01 1.09 −0.64 −0.59
␴yy 62.08 63.06 63.07 0.15 1.02 −1.81 −1.69
␴zz 59.54 64.03 64.06 −0.07 1.19 −0.50 −0.48
␴xy -0.10 0.07 0.00 0.05 0.00 0.01 −0.07
␴yz 0.27 0.43 0.49 0.01 0.04 0.04 0.05
␴zx −1.50 −2.08 −2.30 0.02 0.01 −0.02 0.05
⍀ 396.46 396.46 396.46 434.83 433.74 435.59 435.56
Nion 13 87 15 155 15

algorithm implemented in VASP. The full relaxation with the
compensation for a Pulay stress of 兵−0.64, −1.81, −0.50其
leads to the configuration close to the minimum obtained
from the Murnaghan equation of state.
C. Molecular crystal: Urea
Urea 关共NH2兲2CO兴 共Fig. 3兲 is an example of a molecular
crystal 共space group P4̄21m, No. 113兲, with strong electro-
static and hydrogen bond interactions. In the crystal, the mol-
ecules occupy a special position compatible with the full
molecular symmetry 共mm2兲. High-resolution x-ray44 and
neutron45,46 diffraction studies show small differences in the
cell parameters, but some significant changes in the atomic
positions.
The conventional primitive internal coordinates are gen-
erated only for intramolecular degrees of freedom, the mu-
tual positions of individual urea molecules are described us-
ing the 5 / r coordinates generated as described in the
preceding section. Total number of 152 conventional primi-
tive and 160 inverse-power distance coordinates have been
used to generate the delocalized internal coordinates. The
data concerning this example are collected in Table IV. The
initial configuration has already the correct space group sym-
metry 共P4̄21m兲. As pointed out by Baker et al.,25 delocalized
internal coordinates are automatically symmetry adapted.
Therefore the symmetry is preserved if the relaxation is
started with correct symmetry. As in the previous examples,
Pulay stress causes the underestimation of the equilibrium
cell volume. The structure relaxed with stress compensated
for this effect is very close to the minimum of the Mur-
naghan fit. The performance of our algorithm is by a factor
of 5 better than the native optimizer in VASP.
D. Constrained relaxation: Urea
To illustrate the ability of our algorithm to impose virtu-
ally any geometrical constraint on the structure, we have
chosen example of urea with fixed intramolecular angles and
torsions. The relaxations have been started from the same
configuration as in the previous example. The relaxation cri-
teria are the same as in the unconstrained relaxations. Note,
however, that the contributions to the cartesian gradients cor-
responding to the constrained coordinates had to be projected
out. Results of relaxations of atomic positions, atomic posi-
tions, and lattice parameters, data for the minimum of the
Murnaghan equation of state and for the relaxation with the
correction for the Pulay stress 共estimated in the uncon-
strained relaxations兲 are shown in Table V.

IV. CONCLUSIONS
We have shown that the geometry optimization of peri-
odic systems in internal coordinates offers a highly advanta-
FIG. 3. Tetragonal unit cell of urea, 共NH2兲2CO. geous alternative to perform structural relaxations of solids

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124508-9 Geometry optimization of periodic systems J. Chem. Phys. 122, 124508 共2005兲

TABLE IV. Optimization of the urea structure: the initial configuration 共Initial兲; relaxation of the ionic degrees of freedom using delocalized internal
coordinates 共兵q其兲 and using the VASP native optimizer 共兵s其兲; relaxation of the lattice parameters and ionic positions using delocalized internal coordinates
共兵q , q̂其兲 and with the VASP native optimizer 共兵s , h其兲; minimum of the fitted Murnaghan equation of state 共EOS兲; and the full relaxation using delocalized
internal coordinates with stress corrected for a Pulay stress 共兵q , q̂ ; ␴其兲. Listed are the cell parameters 关a, b, c 共Å兲; ␣, ␤, ␥ 共deg.兲兴, energy 共hartree兲, gradient
共a.u.兲, stress 共kB兲, cell volume 共Å3兲, and the number of relaxation steps.

Parameter Initial 兵q其 兵s其 兵q , q̂其 兵s , h其 EOS 兵q , q̂ ; ␴其

a 5.565共0兲 5.758共2兲 5.744共0兲 5.790共6兲 5.788共6兲

b 5.565共0兲 5.758共2兲 5.744共0兲 5.79共6兲 5.788共6兲
c 4.684共0兲 4.696共9兲 4.695共5兲 4.705共9兲 4.703共6兲
E −3.567 49 −3.579 44 −3.579 42 −3.580 78 −3.580 75 −3.580 81 −3.580 81
gmax 0.075 04 0.000 03 0.000 18 0.000 04 0.000 13 0.000 04 0.000 17
␴xx 79.14 9.38 9.84 −0.02 0.83 −1.17 −1.18
␴yy 79.14 9.38 9.84 −0.02 0.83 −1.17 −1.18
␴zz 145.60 8.18 8.63 0.04 −0.02 −1.75 −1.42
␴xy 0.00 0.00 0.00 0.00 0.00 0.00 0.00
␴yz 0.00 0.00 0.00 0.00 0.00 0.00 0.00
␴zx 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Volume 145.06 145.06 145.06 155.73 154.92 157.80 157.61
Nion 6 27 9 49 9

and surfaces. It has been demonstrated that the present
implementation is able to handle not only atomic position but
also lattice parameter relaxations. The final geometries ob-
tained by the native optimizer of VASP and the internal co-
ordinate optimizer GADGET are the same within the numeri-
cal precision of the electronic code. For the selected model
systems GADGET outperforms the native optimizer by a fac-
tor of 2–10. One has to be aware of the fact that a consider-
able portion of this better performance can be ascribed to the
quality of the initial Hessian guess and to the use of more
efficient optimization algorithms.
The most significant advantage of the internal coordinate
optimization lies undeniably in the handling of constraints,
as demonstrated by the simple examples of rigid molecule
optimization of the urea molecular crystal. In any case,
the possibility of constraining virtually any physically/
chemically motivated combination of internal coordinates
opens a broad field of application of periodic electronic
structure codes to complicated problems, such as phase tran-
sitions, solid state chemical reactions, etc.
The internal coordinate optimizer GADGET is an indepen-
dent software, easy to interface with various molecular and
solid state total energy codes. It allows the user to optimize
not only periodic but also finite 共molecular兲 systems in delo-
calized internal coordinates by ignoring the lattice parameter
block of the extended B-matrix, i.e., by the standard method
widely documented in the literature 共see, e.g., Ref. 12兲. In
addition to the innovative treatment of periodic systems, the
GADGET program includes a large selection of algorithms
permitting the efficient handling of Hessian update, transi-
tion state optimization, etc. An exhaustive overview of these
features will be the subject of a forthcoming paper that de-
scribes the technical aspects of our implementation of these
algorithms in GADGET.

TABLE V. Relaxation of urea with constrained intramolecular angles and torsions: the initial configuration 共Initial兲; relaxation of the ionic degrees of freedom
using delocalized internal coordinates 共兵q其兲; relaxation of the lattice parameters and ionic positions using delocalized internal coordinates 共兵q , q̂其兲; minimum
of the fitted Murnaghan equation of state 共EOS兲; and the relaxation of the lattice parameters and ionic positions using delocalized internal coordinates with
stress corrected for a Pulay stress 共兵q , q̂ ; ␴其兲. Listed are cell parameters 关a, b, c 共Å兲; ␣, ␤, ␥ 共deg.兲兴, energy 共hartree兲, gradient 共a.u.兲, stress 共kB兲, cell volume
共Å3兲, and the number of relaxation steps.

Parameter Initial 兵q其 兵q , q̂其 EOS 兵q , q̂ ; ␴其

a 5.565共0兲 5.768共0兲 5.802共4兲 5.802共7兲

b 5.565共0兲 5.768共0兲 5.802共4兲 5.802共7兲
c 4.684共0兲 4.710共7兲 4.717共3兲 4.716共9兲
E −3.567 49 −3.578 96 −3.580 54 −3.580 57 −3.580 57
gmax 0.075 04 0.000 03 0.000 08 0.000 08 0.000 05
␴xx 79.14 15.17 3.53 2.18 2.12
␴yy 79.14 15.17 3.53 2.18 2.12
␴zz 145.60 1.20 −7.23 −8.23 −8.43
␴xy 0.00 0.00 0.00 0.00 0.00
␴yz 0.00 0.00 0.00 0.00 0.00
␴zx 0.00 0.00 0.00 0.00 0.00
Volume 145.06 145.06 156.72 158.82 158.82
Nion 6 19 17

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124508-10 Bučko, Hafner, and Ángyán J. Chem. Phys. 122, 124508 共2005兲

3
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⳵ ␧ ␮␯ 25
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42
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