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# Symplectic Resolutions for Nilpotent Orbits (II)

## 1 Introduction

Let $`X`$ be a complex variety, which is smooth in codimension 1. Following , the variety $`X`$ is said to have symplectic singularities if there exists a holomorphic symplectic 2-form $`\omega `$ on $`X_{reg}`$ such that for any resolution of singularities $`\pi :ZX`$, the 2-form $`\pi ^{}\omega `$ defined a priori on $`\pi ^1(X_{reg})`$ can be extended to a holomorphic 2-form on $`Z`$. If furthermore the 2-form $`\pi ^{}\omega `$ extends to a holomorphic symplectic 2-form on the whole of $`Z`$ for some resolution of $`X`$, then we say that $`X`$ admits a symplectic resolution, and the resolution $`\pi `$ is called symplectic.

One important class of examples of symplectic singularities consists of nilpotent orbit closures in a semi-simple complex Lie algebra. Projective symplectic resolutions for these singularities have been completely characterized in . This note studies the relationship between two such projective symplectic resolutions.

Recall that two varieties $`Z_1`$ and $`Z_2`$ are deformation equivalent if there exists a flat morphism $`𝒵\stackrel{𝑓}{}S`$ over a connected curve $`S`$ such that $`Z_1`$ and $`Z_2`$ are isomorphic to two fibers of $`f`$. The purpose of this note is to prove the following:

###### Theorem 1.

Let $`𝒪`$ be a nilpotent orbit in a complex simple Lie algebra $`𝔤`$ of classical type . Suppose that $`\overline{𝒪}`$ admits two projective symplectic resolutions $`Z_1\overline{𝒪}`$ and $`Z_2\overline{𝒪}`$. Then $`Z_1`$ is deformation equivalent to $`Z_2`$.

In particular, we see that $`Z_1`$ and $`Z_2`$ are diffeomorphic, thus they have the same topological invariants (Betti numbers etc.), which is in some sense the McKay correspondence for nilpotent orbit closures. Another motivation of this result is to provide support for the following:

###### Conjecture 1.

Let $`X`$ be an irreducible variety with symplectic singularities. Suppose that we have two projective symplectic resolutions: $`Z_1X`$ and $`Z_2X`$. Then $`Z_1`$ is deformation equivalent to $`Z_2`$.

When $`X`$ is projective, this conjecture has been proven by D. Huybrechts (Theorem 4.6 ). In , D. Kaledin proved the conjecture under a rather restrictive hypothesis (Condition 5.1 ). In , we proved that any projective symplectic resolution for a symmetric product $`S^{(n)}`$ of a symplectic connected surface $`S`$ is isomorphic to the Douady-Barlet resolution $`S^{[n]}S^{(n)}`$. In particular, this also verifies the above conjecture. Some other results on uniqueness of symplectic resolutions for some quotient symplectic singularities and for some nilpotent orbit closures are obtained in .

## 2 Key lemma

I am indebted to M. Brion for pointing out the following lemma, which plays a key role in the proof of our theorem.

###### Lemma 1.

Let $`G`$ be a semi-simple complex connected Lie group with Lie algebra $`𝔤`$. Let $`P`$ be a parabolic subgroup of $`G`$ with Levi factor $`L`$. Then $`T^{}(G/P)`$ is deformation equivalent to $`G/L`$.

Proof. We first show that $`T_o^{}(G/P)`$ is deformation equivalent to $`P/L`$ as $`P`$-varieties, where $`o`$ is a base point of $`G/P`$. Let $`𝔭_u`$ be the Lie algebra of the unipotent radical $`P_u`$ of $`P`$. Then $`𝔭_u`$ equipped with the adjoint action of $`P`$ is identified with $`T_o^{}(G/P)`$.

Let $`z`$ be an element in the center of $`ł:=\mathrm{Lie}(L)`$ such that its centralizer in $`G`$ is exactly $`L`$, then its centralizer in $`𝔤`$ is exactly $`ł`$. Consider the family $`V:=(tz+𝔭_u)_tf`$ of sub-spaces in $`𝔤`$. Note that each subspace $`tz+p_u`$ is stable under the adjoint action of $`L`$ and the adjoint action of $`P_u`$ (since $`[z,𝔭_u]`$ is contained in $`𝔭_u`$). Thus we get a family of $`P`$-varieties with $`𝔭_u`$ being the special fiber.

Now we show that $`tz+𝔭_u`$ is isomorphic to $`P/L`$ for $`t0`$. In fact, the $`P`$-orbit of $`tz`$ coincides with the $`P_u`$-orbit of $`tz`$, which is closed in $`𝔤`$ (since $`P_u`$ is unipotent), but $`Ad(P_u)tz`$ and $`tz+𝔭_u`$ have the same tangent spaces at $`tz`$, thus $`Ad(P_u)tz`$ is also open in $`tz+𝔭_u`$, which shows that $`tz+𝔭_u`$ is exactly the $`P`$-orbit of $`tz`$. By our choice of $`z`$, the latter is isomorphic to $`P/L`$.

Now consider the family $`G\times _PV`$, which is given by $`(g,v)Pf(v)`$. Then the central fiber is $`T^{}(G/P)`$ and other fibers are all isomorphic to $`G/L`$, which concludes the proof. $`\mathrm{}`$

###### Remark 1.

Notice that if two parabolic subgroups $`P_1`$ and $`P_2`$ have a Levi factor $`L`$ in commun, then the two deformations $`G\times _{P_1}V_1`$ and $`G\times _{P_2}V_2`$ have the same fibers over $`\{0\}`$.

###### Remark 2.

The natural morphism

$$G\times _PV\stackrel{\stackrel{~}{\pi }}{}W_P𝔤,(g,v)Ad(g)v$$

gives a deformation of the Springer resolution $`\pi :T^{}(G/P)\overline{𝒪},`$ where $`W_P`$ is the image of $`\stackrel{~}{\pi }`$, depending a priori on the polarization $`P`$. Notice that $`\stackrel{~}{\pi }_t`$ is an isomorphism if $`t0`$.

## 3 Proof of the theorem

First let us recall the following theorem from :

###### Theorem 2.

Let $`𝒪`$ be a nilpotent orbit in a semi-simple complex Lie algebra $`𝔤`$ and $`G`$ a connected Lie group with Lie algebra $`𝔤`$. Suppose that $`\overline{𝒪}`$ admits a symplectic resolution $`Z\overline{𝒪}`$. Then $`Z`$ is isomorphic to $`T^{}(G/P)`$ for some parabolic subgroup $`P`$ of $`G`$ and under this isomorphism, the map $`ZT^{}(G/P)\overline{𝒪}`$ becomes the natural collapsing of the zero section.

Such a parabolic sub-group $`P`$ is called a polarization of $`𝒪`$ in . So to prove Theorem 1, we need to show that if we have two polarizations $`P_1,P_2`$ of $`𝒪`$ such that $`T^{}(G/P_1)`$ and $`T^{}(G/P_2)`$ are birational to $`𝒪`$, then $`T^{}(G/P_1)`$ is deformation equivalent to $`T^{}(G/P_2)`$. In fact, we will prove that either $`P_1`$ and $`P_2`$ have conjugate Levi factors or $`G/P_1`$ is isomorphic to $`G/P_2`$ (in some cases of $`𝔤=𝔰𝔬_{2n}`$). Then Lemma 1 will conclude the proof.

To this end, we will do a case-by-case check, using the results of W. Hesselink in . Let d=$`[d_1,\mathrm{},d_N]`$ be the partition corresponding to the orbit $`𝒪`$ (c.f. section 5.1 ). Let s = $`[s_1,\mathrm{},s_k]`$ be the dual partition of d, where $`s_i=\mathrm{\#}\{j|d_ji\}`$.

### 3.1 Case $`𝔤=𝔰𝔩_n`$

Let $`V=^n`$. A flag $`F`$ of $`V`$ is a sequence of sub-spaces $`0=F_0F_1\mathrm{}F_k=V`$. Its type is the sequence $`(p_1,\mathrm{},p_k)`$ given by $`p_i=dim(F_i/F_{i1})`$. One shows easily that the stabilizer $`PG`$ of $`F`$ is a parabolic subgroup.

By Theorem 3.3 , any polarization $`P`$ of $`𝒪`$ is a stabilizer of such a flag $`F`$ with type $`(s_{\sigma (1)},\mathrm{},s_{\sigma (k)})`$ for some permutation $`\sigma 𝔖_k`$, and they have conjugate Levi factors.

### 3.2 Case $`𝔤=𝔰𝔭_{2n}`$

Let $`V=^{2n}`$ and $`\varphi `$ a non-degenerate anti-symmetric bilinear form on $`V`$. A flag $`F=(F_0,\mathrm{},F_k)`$ is called isotropic if $`F_i^{}=F_{ki}`$ for $`0ik`$, where $`F_i^{}`$ is the orthogonal space of $`F_i`$ with respect to the bilinear form $`\varphi `$. The type $`(p_1,\mathrm{},p_k)`$ of an isotropic flag satisfies $`p_i=p_{k+1i}`$ for $`1ik`$. By Lemma 4.3 , every parabolic subgroup $`P`$ of $`G`$ is the stabilizer of some isotropic flag, and two parabolic subgroups with the same flag type are conjugate under the action of $`G`$ (Lemma 4.4 loc. cit.).

Here all congruences are modulo 2. For an even number $`q`$, let

$$Pai(2n,q)=\{partitions\pi of\mathrm{\hspace{0.17em}2}n|\pi _j1ifjq;\pi _j0ifj>q\}.$$

The union $`Pai(2n)=_qPai(2n,q)`$ parametrizes all conjugate classes of Levi factors of parabolic subgroups in $`G`$. For any $`q`$, there exists an injective Spaltenstein mapping (Proposition 6.5 )

$$S_q:Pai(2n,q)𝒫_1(2n),$$

where $`𝒫_1(2n)`$ is the set of partitions of $`2n`$ in which odd parts occur with even multiplicity (cf. Section 5.1 ).

By the proof of Proposition 3.21 , if $`P`$ is a parabolic subgroup of $`G`$ such that $`T^{}(G/P)`$ gives a symplectic resolution for $`\overline{𝒪}`$, then one has $`q=\mathrm{\#}\{j|d_j1\}`$. The injectivity of the map $`S_q`$ implies that any two such parabolic subgroups $`P_1`$ and $`P_2`$ have conjugate Levi factors.

### 3.3 Case $`𝔤=𝔰𝔬_{2n+1}`$

Let $`V=^{2n+1}`$ and let $`\varphi `$ be a non-degenerate symmetric bilinear form on $`V`$. In the same way as in the case of $`𝔤=𝔰𝔭_{2n}`$, one defines the notion of isotropic flags. The proof goes in a similar way as in the case of $`𝔤=𝔰𝔭_{2n}`$.

### 3.4 Case $`𝔤=𝔰𝔬_{2n}`$

Let $`V=^{2n}`$ and $`\varphi `$ a non-degenerate symmetric bilinear form on $`V`$. The group $`H`$ of automorphisms of $`V`$ preserving $`\varphi `$ has two components. The identity component of $`H`$ is our Lie group $`GSO(2n)`$.

By Lemma 4.4 , the class of parabolic subgroups of $`G`$ with flag type $`(p_1,\mathrm{},p_k)`$ splits into two conjugacy classes (denoted by $`P_1`$ and $`P_2`$) under the action of $`G`$ if and only if $`k=2t`$ and $`p_t2`$. Furthermore, the two parabolic subgroups are conjugate under the action of $`H`$, i.e. there exists an element $`hH`$ such that $`P_2=hP_1h^1`$. Take an isotropic flag $`F=(F_0,\mathrm{},F_k)G/P_1`$, then $`F^{}=hF=(hF_0,\mathrm{},hF_k)`$ is an isotropic flag in $`G/P_2`$. This gives an isomorphism between $`G/P_1`$ and $`G/P_2`$.

So we need only to consider polarizations of $`𝒪`$ with different flag types. By the proof of Proposition 3.22  and the proof of Lemma 4.6 , two such polarizations have conjugate Levi factors..

## 4 Concluding remarks

4.1 Though we believe that Theorem 1 is also true for exceptional Lie algebras, by lack of a complete description of polarizations of their nilpotent orbits, we don’t know how to check this.

4.2 One should bear in mind that for two symplectic resolutions $`Z_i\overline{𝒪},i=1,2,`$ though $`Z_1`$ is deformation equivalent to $`Z_2`$, $`Z_1`$ and $`Z_2`$ may be non-isomorphic. An explicit example is given in .

4.3 By Remark 1, our theorem can be strengthened as follows: Let $`Z_i\overline{𝒪},i=1,2,`$ be two symplectic resolutions for a nilpotent orbit closure in a simple complex classical Lie algebra. Then there exists two deformations $`𝒵_i,`$ such that $`𝒵_{i,0}Z_i`$ and $`𝒵_{1,t}𝒵_{2,t}`$ for any $`t0`$. This can be viewed as an analogue of the result of D. Huybrechts (Theorem 4.6 ).

4.4 A stronger form of Conjecture 1 is stated in , where we conjectured that there exist deformations $`F_i:𝒵_i𝒳`$ of the morphisms $`\pi _i:Z_iX`$, such that $`F_{i,t}`$ is an isomorphism for $`t0`$. In the case of nilpotent orbit closures in $`𝔰𝔩_n`$, we proved this in , by constructing explicitly the deformations. For the other cases, though by Remark 2 we have a deformation $`\stackrel{~}{\pi }`$ of $`\pi `$, we don’t know whether the deformation spaces $`W_P`$ of $`\overline{𝒪}`$ are isomorphic or not for two polarizations.

Acknowledgments: I want to thank A. Beauville, M. Brion and Y. Namikawa for helpful discussions and suggestions. It was pointed out to me by Y. Namikawa that there was an error in an earlier version of this note. Then M. Brion suggested to me the Key lemma to complete the proof.

Baohua Fu,
Labortoire J. A. Dieudonné, Parc Valrose
06108 Nice cedex 02, FRANCE
baohua.fu@polytechnique.org


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# Global protein function prediction in protein-protein interaction networks

## Experimental protocol

To each unclassified protein $`i=1,2,\mathrm{},n`$ a function si is assigned, chosen among the $`F`$ possible ones in order to globally minimize the following score function:

$$E=\underset{i,j}{}J_{ij}\delta (\sigma _i,\sigma _j)\underset{i}{}h_i(\sigma _i),$$
(1)
where $`J_{ij}`$ is the adjacency matrix of the interaction network for the unclassified proteins ($`J_{ij}`$ is equal to 1 if protein $`i`$ and $`j`$ interact and are unclassified, 0 otherwise), $`\delta (i,j)`$ is the discrete delta function and $`h_i(\sigma _i)`$ is the number of classified partners of protein $`i`$ with function $`\sigma _i`$.

The “majority rule” of  corresponds to minimize solely the second term on the r.h.s. of equation (1). The above can be achieved with local methods (i.e. considering successively and independently each protein). In our method, the contribution to the total score of assigning a protein $`i`$ to functional class $`\sigma _i`$ depends also on the assignment made to all other proteins, resulting in a much harder computational task. The advantage is that the underlying requirements that “interaction requires a common function” is applied also to interactions between previously unclassified proteins, that are completely ignored with the majority rule approach.

To overcome the computational difficulties and find the configuration or configurations that minimize $`E`$ we perform a simulated annealing  introducing an effective temperature $`T`$. We start with an initial random configuration $`\sigma _i`$. Then, at each Monte-Carlo step, we select one protein at random and change its state from si to $`\sigma _i^{}`$, where $`\sigma _i^{}`$ is selected at random among the possible states of protein $`i`$ with the constraint $`\sigma _i^{}\sigma _i`$. We then compute the score difference $`\mathrm{\Delta }E=E^{}E`$ between these two configurations. If $`\mathrm{\Delta }E0`$ we accept the new configuration. If $`\mathrm{\Delta }E>0`$, we accept the new configuration with probability $`r=exp(\mathrm{\Delta }E/T)`$ or keep the original configuration with probability $`1r`$. This Monte-Carlo step is repeated until $`E`$ reaches a stationary value. Thereafter, $`T`$ is decreased by a tiny amount. These two process, equilibration at a given $`T`$ and decrease of $`T`$ is repeated until the protein states remain unchanged for a sufficiently long time. At the end the protein states are our predicted functional classification. Since the the minimum energy solution is not unique the simulated annealing process has been repeated several times, starting from different initial configurations. Finally we computed the fraction of times pis the protein i was observed in the final state s, which give us an estimate of the probability that protein i belongs to the functional classification s. References


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# Disks around the Young Stars TW Hya and HD 100546 Imaged at 3.4 Millimeters with the Australia Telescope Compact Array

## 1 Introduction

Many young stars exhibit emission from circumstellar dust particles distributed in disks with properties similar to the early Solar System, and much activity is currently devoted to characterizing the physical properties of these disks to extract information on planet formation. Observations at millimeter wavelengths are especially important because the disk material beyond a few stellar radii is at temperatures from a few hundreds to a few tens of degrees, and the physical and chemical conditions can be probed in detail in this part of the spectrum (see reviews by Beckwith & Sargent 1996, Wilner & Lay 2000, Langer et al. 2000).

The recent upgrade of the Australia Telescope Compact Array (ATCA) with receivers for the 3 mm atmospheric window provides a new opportunity for high resolution imaging of protoplanetary disks located in the southern sky that are difficult or impossible to observe with the millimeter arrays located in the northern hemisphere. The ATCA millimeter-wave upgrade is in progress, and the completed facility will ultimately rival the northern interferometers in sensitivity and angular resolution (see Wong & Melatos 2002 for a more complete description). Now, three of the array antennas are equipped with 3 mm band InP MMIC receivers, and an interim local oscillator system allows for tuning in two ranges between 85 and 91 GHz. We present interferometric observations of dust continuum and HCO+ J=1–0 line emission at 89 GHz from two southern disk targets: (1) TW Hya, the closest known classical T Tauri star, and (2) HD 100546, a nearby Herbig Be star whose infrared spectrum shows crystalline silicates, indicative of comet-like dust.

TW Hya has received a lot of recent observational attention, largely on account of its close proximity. At a distance of $`56\pm 7`$ pc (Hipparcos), TW Hya is almost three times closer than the classical T Tauri stars associated with nearby dark clouds like Taurus and Ophiucus, which makes it an especially attractive target for observations with high angular resolution. At an age of $`10`$ Myr, the TW Hya disk appears to be substantially evolved, with indications of significant grain growth. TW Hya is isolated from any molecular cloud but retains a face-on molecular disk visible in scattered light (Krist et al. 2000, Trilling et al. 2001, Weinberger et al. 2002) that extends to a radius of at least $`3\stackrel{}{\mathrm{.}}5`$ (200 AU). The inner disk of TW Hya has been resolved in dust emission by the VLA at 7 mm (Wilner et al. 2000), and its spectral energy distribution has been modeled extensively (Calvet et al. 2001). The available data are well fitted by an irradiated accretion disk with a developing gap of radius $`4`$ AU, interior to which dust coagulation and settling have rendered the disk optically thin.

The isolation of the TW Hya system from any surrounding molecular cloud material facilitates the study of its physical and chemical structure. The TW Hya disk has been detected in a suite of molecular species (CO, HCN, CN, and HCO+) at submillimeter wavelengths using single dish telescopes (Kastner et al. 1997, van Zadelhoff et al. 2001). More recent, deeper, observations have also detected emission from H13CO+ and DCO+, which indicate deuterium fractionation in the disk similar to cold cores and pristine cometary material (van Dishoeck et al. 2003). So far, no observations have been made that spatially resolve the molecular gas surrounding TW Hya. Such spatially resolved observations are important to verify underlying constructs of the models used to interpret the single dish data, since the physical conditions are subject to strong radial and vertical gradients, which result in considerable chemical complexity.

HD 100546, among the nearest Herbig Ae/Be stars at $`103\pm 6`$ pc (Hipparcos), appears nearby the dark cloud DC296.2-7.9 (Hu, The & de Winter 1989) and shows a disk-like scattered light distribution (Pantin, Waelkens & Lagage 2000, Augereau et al. 2001, Grady et al. 2001) of substantial size, about $`8^{\prime \prime }`$ (8000 AU), as well as strong millimeter emission from dust (Henning et al. 1994, 1998). This relatively isolated system is thought to have an age of $`10`$ Myr (van den Ancker et al. 1997). However, analysis of the full spectral energy distribution suggests the presence of an extended envelope (Henning et al. 1994). Mid-infrared spectroscopy from ISO shows remarkably strong crystalline silicate bands, similar to those observed in comet Hale-Bopp (Malfait et al. 1998) and indicative of unusual and substantial processing of the dust within the disk (Bouwman et al. 2003). Millimeter interferometry has the potential to show directly the presence of a disk component that contains the bulk of the system mass.

## 2 Observations

We observed TW Hya and HD 100456 at 89 GHz (3.4 mm) with the ATCA during the 2002 austral winter using two compact configurations of three 22 meter diameter antennas equipped with millimeter receivers. Table 1 summarizes the observational parameters.

The ATCA observations provided 6 independent east-west baselines with lengths ranging from 22 to 230 meters, resulting in $`2^{\prime \prime }`$ resolution. For each observation, the target pointing center was set to be $`5^{\prime \prime }`$ west of the star position. The digital correlator was configured for two dual polarization bands: (1) a wide band with 33 channels spanning the maximum bandwidth of 128 MHz for continuum sensitivity, and (2) a narrow band with 256 channels over 16 MHz to provide high frequency resolution on the HCO+ J=1–0 line, which is one of the few potentially detectable spectral lines accessible to the interim system. The sky signal is mixed with a Gunn oscillator locked at 80505.5 MHz and passed through an X-band (8000-10800 MHz) filter and splitter module, which results in an accessible frequency range of 88.506 to 91.305 GHz. A new local oscillator system under construction will allow coverage of the frequency range 85 to 105 GHz, with a possible extension to 115 GHz.

All calibration and imaging was performed with the MIRIAD software. Complex gains were derived from frequent observations of nearby quasars. Because the narrow band provided low signal-to-noise ratios on the quasars, a phase offset between the wide band and narrow band was determined from short observations of a strong source on each day, either J0423-012 or J0538-440. These short observations of strong sources were also used to determine the bandpass response. For TW Hya, additional weaker quasars located close to the star were included in the observing sequence to provide an empirical check on the atmospheric seeing and effectiveness of the phase calibration. Typical system temperatures were 300 to 400 K (SSB), with higher values at low elevations. The flux densities were set with reference to the planet Mars; the scatter in derived fluxes on consecutive days suggests uncertainties of approximately 20%.

Images were made of the sum of the two linear polarizations using natural weighting to obtain best sensitivity. All images were cleaned to a cutoff of twice the r.m.s. noise level. Because Doppler tracking was not applied during the observations, the correspondence between individual frequency channels and velocity changes with time during the course of the observations. Therefore, the spectral data were imaged in resampled velocity bins of 0.5 km s-1 width, coarse compared to these changes, rather than individual frequency channels.

## 3 Results

### 3.1 TW Hya

Figure 1 shows the 89 GHz continuum emission detected from TW Hya. The position is coincident with the optical star and radio detections at longer wavelengths. A Gaussian fit to the visibilities gives a flux of $`41\pm 4`$ mJy (random error only) and an apparent size consistent with an unresolved source slightly broadened by the phase noise on the longer baselines. This Gaussian fit is also compatible with the extended disk seen in scattered light, since the dust emission from the circumstellar disk is strongly centrally peaked by the combination of low opacity and increasing column density and temperature towards the star (see Mundy et al. 1996; Wilner et al. 2000).

The TW Hya 89 GHz continuum flux measurement agrees well with expectations from previously reported measurements at both higher (350 GHz) and lower (43 GHz) radio frequencies (Weintraub, Sandell & Duncan 1989, Wilner et al. 2000, Wilner 2001). In addition, it is consistent with predictions of various disk models based on the radio observations that contain a population of large dust grains to account for the shallow spectral slope with power law index $`3`$ observed in this frequency range (Trilling et al. 2001, Calvet et al. 2002). The good fit of the new 89 GHz measurement with expectations gives confidence in the reliability of the ATCA system, and the accuracy of the absolute flux scale.

Figure 2 shows a series of images in four velocity bins for the HCO+ J=1–0 line emission near LSR velocity $`3`$ km s-1. A narrow line emission feature is clearly visible at the stellar position with a velocity and linewidth commensurate with previously reported molecular line detections from the face-on disk, which have $`V_{\mathrm{LSR}}`$=2.9 km s-1 and $`\mathrm{\Delta }V0.6`$ km s-1. Figure 3 shows the spectrum at the continuum position. The peak line flux at 0.5 km s-1 resolution is 0.40 Jy, which corresponds to a brightness temperature of 4.3 K in the $`6\stackrel{}{\mathrm{.}}9\times 2\stackrel{}{\mathrm{.}}1`$ beam. The line emission from the disk is clearly spatially resolved; a circular Gaussian fit to the visibilities in a 0.5 km s-1 bin gives a full-width at half maximum size of $`3\stackrel{}{\mathrm{.}}2\pm 0\stackrel{}{\mathrm{.}}8`$.

### 3.2 HD 100546

Figure 4 shows the 89 GHz continuum emission detected from HD 100546. The peak position is coincident with the star to better than $`1^{\prime \prime }`$. A fit to the visibilities gives a point source flux of $`36\pm 3`$ mJy at the star position. The residuals to this fit provide a hint that additional emission is present. The image shows an extra peak of low significance located $`7^{\prime \prime }`$ to the southeast. This additional peak may be related to the slight extension seen in the single dish 1.3 mm bolometer image of Henning et al. (1998). Extensions along the same position angle are also visible in scattered light, in particular in the sensitive HST/STIS images of Grady et al. (2001), where nebulosity can be seen to extend from the northwest to the southeast. No line emission is detected to a limit of 0.17 Jy per channel ($`3\sigma `$), either at the LSR velocity of the cloud DC296.2-7.9 of 3.6 km s-1 (Otrupcek, Hartley & Wang 2000), or at the stellar LSR velocity of about -1 km s-1, which derives from the heliocentric “astrometric” radial velocity of $`9\pm 1`$ km s-1 determined from Hipparcos (Madsen 2002).

## 4 Discussion

### 4.1 TW Hya

The spatially resolved observations of the HCO+ J=1–0 emission from TW Hya allow for a check of the basic paradigm that trace molecules are present in an extended upper layer of the disk, with overall abundances depleted with respect to molecular hydrogen by large factors by comparison with those of interstellar dark clouds (Aikawa & Herbst 1999, Willacy & Langer 2000, Aikawa et al. 2002). In the disk midplane, which contains most of the mass, the combination of high densities and low temperatures results in nearly all trace molecules sticking to grain surfaces and disappearing from the gas. At the disk surface, the molecules are photo-dissociated. In between, below the surface, is a layer that is warm and shielded from stellar radiation and activity where molecules survive and abundances peak.

The TW Hya disk structure and chemistry has been considered in detail by van Zadelhoff et al. (2001), whose model calculations suggest that the depletion of species like CO and HCO+ results from a combination of photodissociation in the warm surface layers and freezing-out in the cold, dense parts of the disk. In these models, the molecular emission largely originates from the region just below the disk surface where the HCO+ abundance climbs to a few times $`10^{10}`$. In general, the HCO+ abundance follows the CO abundance in the disk, since its formation is primarily from CO reacting with H$`{}_{}{}^{+}{}_{3}{}^{}`$, with destruction by dissociative recombination with free electrons.

Figure 5 shows the visibility amplitude of the HCO+ J=1–0 emission from TW Hya as a function of baseline length; the falloff at longer baselines demonstrates that the emission region is resolved. A circular Gaussian FWHM “size” of $`3\stackrel{}{\mathrm{.}}2`$ provides a crude description of the full line brightness distribution. Figure 5 includes the visibility amplitudes derived from four of the favored models of van Zadelhoff et al. (2001), which provide reasonable fits to higher-J HCO+ single dish observations. Two models are based on the radiatively heated accretion disk structure of D’Alessio et al. (1999), and two models are based on the passive two-layer description of Chiang & Goldreich (1997). Two chemical scenarios are presented for each of these physical models. The interstellar HCO+ abundance is assumed to be $`5\times 10^9`$, and in one model HCO+ is depleted by a factor of 100 with an additional order of magnitude drop when the temperature falls below 20 K, while in another model HCO+ is depleted by a factor of 500 throughout. Table 2 summarizes the models. Figure 5 shows that all of these models, which have disk masses of 0.03 $`M_{}`$ and disk radii of 200 AU, agree well with the ATCA observations, for both the size scale and the absolute intensity of the HCO+ line emission. (Note that visibility amplitude is a positive definite quantity, which results in a positive bias in Figure 5.)

Figure 6 provides another view of the four models in the form of synthetic images. These images were made by sampling each of the models with the same visibility distribution as obtained by the ATCA observations, taking a 0.5 km s-1 bin centered on the line. These images may be compared with the panel in Figure 2 for LSR velocity 2.75 km s-1, where the line emission peaks. In this view, it is not easy to see that the line emission is well resolved spatially, but the similarity of the models in overall brightness and spatial extent is clearly apparent.

While none of the models of van Zadelhoff et al. (2001) were fine-tuned to match all of the available constraints, and none provides a unique best fit to the ATCA data, the high HCO+ depletion factors are a robust feature. All four models are indistinguishable within the noise of the observations, though there are differences in detail in the visibility distributions among the models. There is perhaps a hint that the models that produce the more concentrated emission distributions are best. The model curves in Figure 5 suggest that resolved observations with better signal-to-noise have the potential to discriminate between subtly different physical and chemical scenarios.

HCO+ depletions of an order of magnitude or more have been inferred for other T-Tauri systems from millimeter imaging and analysis, in particular the disks around the GG Tau binary (Guilloteau, Dutrey & Simon 1999) and around LkCa15 (Duvert et al. 2000, Qi 2001). These isolated pre-main-sequence systems are located in holes of the Taurus dark cloud complex, which make their disks readily accessible without confusion. The radii of the gas disks in these systems, $``$800 AU and $``$600 AU, respectively, are among the largest known, and larger by factors of 3 to 4 than the $`200`$ AU radius disk surrounding TW Hya. That the depletion is similarly high in all of these disks provides further evidence that substantial depletion must occur in the dense shielded midplane material, rather than simply in the colder, outer parts of the disks.

Since the critical density of the HCO+ J=1–0 line for collisional excitation is $`6\times 10^4`$ cm-3, the detection of extended emission indicates high densities must be present to large radii, independent of any detailed physical and chemical model for the disk. This in situ measurement of local density confirms indications from scattered light models and also analysis of dust emission that relied on extrapolation of the inner disk density distribution. Resolved images of multiple transitions of multiple species may be used to constrain the disk mass (see Dutrey, Guilloteau and Guelin 1997).

### 4.2 HD 100546

For HD 100546, the spherical radiative transfer models of Henning et al. (1994) that reproduce the far-infrared emission do not account for the observed millimeter flux, even with a population of “fluffy” dust grains, which suggests that a circumstellar disk component must be present in the system. The compact 89 GHz dust continuum emission detected in the ATCA observations provides direct evidence for this disk. An extrapolation of the 1.3 mm flux of 0.69 Jy (Henning et al. 1998) to 89 GHz gives 40 mJy, for a dust opacity power law index near unity, compared with our detected flux of $`36\pm 3`$ mJy. Thus, the disk component nominally accounts for a substantial fraction of the detected 89 GHz flux, though the uncertainties are large. Detailed modeling of the disk properties awaits additional millimeter and submillimeter observations with sufficient angular resolution to separate the disk and envelope components.

The similar continuum fluxes of HD 100546 and TW Hya suggest that the disk in the more distant and warmer HD 100546 system is substantially more massive than the disk around TW Hya. Since HCO+ J=1-0 emission is not detected from HD 100546 with comparable sensitivity to the TW Hya detection, it is likely that the abundance reduction is even more extreme. Perhaps photodissociation of CO in the disk atmosphere is enhanced in the environment of this more massive, hotter star.

Grady et al. (1997) suggest that much of the accreting gas seen in the optical along the line-of-sight to HD 100546 is associated with star-grazing planetesimals, such as comets or asteroids. This may explain both the lack of observed boundary-layer emission, which might be expected from accretion of mostly gaseous material, and signatures of bipolar outflow in forbidden line emission that is characteristic of an optically thick, gaseous accretion disk. This fact, together with the non-detection of HCO+ emission and the highly processed nature of the dust around HD 100546, perhaps indicates that the gas is nearly fully depleted in the disk, in which case the planet building process may be well advanced.

## 5 Conclusions

We have made high resolution observations of the nearby young stars TW Hya and HD 100546 with the ATCA using three antennas equipped at 89 GHz. These observations indicate the promise for future millimeter-wave observations of protoplanetary disks located deep in the southern sky. The observations of the TW Hya disk resolve emission from the HCO+ J=1–0 line, and the measured extent and brightness support disk models with high depletion factors inferred from previous, spatially unresolved, measurements of higher J transitions. The detailed modeling of the TW Hya disk represents a first step towards probing the gas content of this important system, whose dispersal and chemistry may be similar to the early Solar System. A more complete understanding of the details of disk chemistry will require spatially resolved images with higher sensitivity, eventually sampling species that probe all of the relevant chemical families.

Thermal dust continuum emission from these sources was easily detected and promises to be resolved with observations using longer baselines. The available ATCA antenna stations will offer baselines up to 1.5 km in length, corresponding to an angular resolution better than $`0\stackrel{}{\mathrm{.}}5`$ at this frequency, which will be adequate to probe the disk surface density and to start to disentangle disk structure from opacity effects. Both TW Hya and HD 100546 will be prime protoplanetary disk targets for the Atacama Large Millimeter Array, the next generation millimeter interferometer sited in northern Chile, whose construction has just started and will continue for the next decade.

We thank an anonymous referee for several suggestions that improved this paper. The Australia Telescope Compact Array is part of the Australia Telescope, which is funded by the Commonwealth of Australia for operation as a national facility managed by CSIRO. Partial support for this work was provided by NASA Origins of Solar Systems Program Grant NAG5-11777, by the NRAO Foreign Telescope Travel Fund Program, by a NOVA network 2 grant and a NWO-Spinoza grant. CMW acknowledges support of an Australian Research Council Fellowship.


text:
# Flavor Democracy: On Which Basis?

## I Introduction

The physics of flavor is difficult. There are many open questions and the general hope is that the upcoming experiments might shed some light onto this now-obscure part of particle physics. The major issue is to undesrstand the Cabibbo-Kobayashi-Maskawa mixing matrix (CKM) of quarks in the charged weak current as well as the hierarchy in the quark masses. While the two are obviously related the efforts to find quark mass matrices and the resulting CKM is beset with difficulties mainly because the problem is infact infested with many-to-one relations. One reason (albeit rather overlooked) for this is the fact that one can define another physically equivalent mass matrix, by unitary transformations of the quark fields, that might look like anything but the original one. The possibilities are not only these: one could also write down mass matrices in a basis where there is an ad-hoc CKM (not obviously the final physical one). These considerations clearly do not contain new physics but aim at somewhat simplifying a problem that is already rather difficult. Sticking to the weak eigenbasis to write down mass matrices might actually be helping the problem remain difficult. The idea here is similar to Legendre of Fourrier transformations of differential equations: although the physics remain the same the problem ”look” simpler when transformed. In this short letter I will try to demonstrate that there are certain priviledged basises on which the problem of quark mass matrices and the CKM look simpler.

## II The Argument

Consider the ”physical” charged electroweak and mass lagrangian:

$$W_\mu \overline{U}\gamma ^\mu (1\gamma ^5)KD+\overline{U}M_U^{diag}U+\overline{D}M_D^{diag}D.$$
(1)
Here $`K`$ is the physical CKM and the diagonal quark mass matrices contain the physical quark masses. Now let us remember that there is a $`SU(3)`$ matrix such that its elements have equal norm

$$K_d\frac{1}{\sqrt{3}}\left[\begin{array}{ccc}e^{i\pi /6}& e^{i\pi /6}& 1\\ e^{i\pi /6}& e^{i\pi /6}& 1\\ 1& 1& i\end{array}\right]$$
(2)
This matrix is defined modulo permutations of its rows(columns) and it can be sandwiched between two different diagonal $`SU(3)`$ matrices which would introduce 4 arbitrary phases.

Now consider rotating the quark fields by matrices similar to the one above. Unless there are magical cancellations the largest (up-down) quark mass will infest the resulting (up-down) mass matrices. Also for the CKM the hierarchy will disappear. This transformation consequently will switch to a basis in which the mass matrices are somewhat (as far as the norms are concerned) democratic and an ad-hoc CKM that with hierarchy smeared. It then follows that ”flavor” democracy is not a ”mere” assumption: it does exist to some extend in some basis given there is a large hierarchy of quark masses. The physical meaning of this internediate basis may be non-existent. Since the ultimate aim is to go to the mass eigenbasis, it is to be considered as a do-nothing-but-for-something.

This point of view has the following advantage, since in the democratic basis only the largest quark masses will dominate the mass matrices the only parameters that would remain if not to be considered a ”perturbation” are the phases of the quark mass matrices. There are four phases in a norm-democratic mass matrix in one (up-down) sector. One is coming from the Nuyts’ theorem (J. Nuyts, Phys. Rev. Lett.26, 1604, (1971).), that is the non-hermitean part is a multiple of identity (this is true for the full mass matrix with up and down quarks combined) and the other three are coming from the hermitean part of which two (separately for up and down sectors) may be transformed away by the definition ambiguity (four phases) of the ad-hoc CKM. Thus the final form of a mass matrix in the democratic basis (ignorig norm perturbations) is

$$M^{democ}=m_3\left[\begin{array}{ccc}e^{i\varphi }& e^{i\chi }& 1\\ e^{i\chi }& e^{i\varphi }& 1\\ 1& 1& e^{i\varphi }\end{array}\right]$$
(3)
The location of $`\chi `$ is arbitrary and introduces a discrete definition ambiguity. Also although we know that experimentally $`ArgDet(M)<10^{10}`$ we keep the Nuyts’ phase here nevertheless for completeness.

## III The choices for the ad-hoc CKM

The crucial matter is then to pick an ad-hoc CKM in the democratic basis. It is clear that the matrix in Eq.2 is not ultimately a choice because we argued about rotating the original CKM with it in the first place to go to the democratic basis. But our aim can seldom be to recover the ”original” CKM via this route. This is impossible. The idea is to find a CKM via this method that would serve as a solution around which mass ratio effects will be considered a perturbation. What is interesting is that this solution might have physical relevance for flavor physics.

Within the idea of democracy the choices for the ad-hoc CKM are not limited to the $`K_d`$ defined in Eq.2, since unitraity tends to frustrate democracy. But we can still do as much as we can. For example let us consider the following ad-hoc CKM

$$\frac{1}{3}\left[\begin{array}{ccc}1& 2& 2\\ 2& 1& 2\\ 2& 2& 1\end{array}\right]$$
(4)
This matrix is absolutely out of hierarchy thus I consider it to be democratic. Accidentally this matrix commutes with the democratic mass matrix of 3 if $`\chi `$ and $`\varphi `$ are taken to be zero. Thus the ”would-be physical” CKM of this toy model is the unit matrix. This example demonstrates that the phases $`\chi `$ can be used to explore the less (wrt to a unit matrix) hierarchical results.

One can actually generalize the idea of democratic unitary matrices by defining matrices of the form,

$$\left[\begin{array}{ccc}a& b& c\\ b& a& d\\ c& d& a\end{array}\right]$$
(5)
The case with $`a=b=c=d`$ ans with $`b=c=d`$ are given in Eq.2 and Eq.4 respectively. For other solutions, when one also would like to introduce non-trivial phases,the elements should not differ by large order of magnitudes since one indeed solves a system of equation without small or large numbers. This idea can be further generalized but I do not wish to get in detail here since this is not a full research article but rather a rapid communication.

## IV A toy Application

Let us consider a toy application. Take the ad-hoc CKM to be $`K_d^{1/3}`$ (this is within the idea of democratic unitary matrices) and the mass matrices to be just composed of 1’s. There is one caveat here. The eigenvalues of the mass matrix are $`\{0,0,3\}`$ and one has to face the null space redundancy for choosing the diagonalization matrices. However we can still invoke democratic point of view and say that the zero mass states share the null-space in a ”democratic” way that is they both take null space vectors rotated with $`\pi /4`$. The resulting CKM has the following form

$$\left[\begin{array}{ccc}0.98& 0.20& 0.03\\ 0.20& 0.98& 0.10\\ 0.03& 0.10& 0.99\end{array}\right]\mathrm{and}\delta \pi /2$$
(6)
There was fine tuning of no parameters, yet the Cabibbo angle is well near the physical value and there is some hierarchy in the third columns.

## V Conclusion

The argument here is that there is always a basis in which the mass matrices will be near norm-democratic. The point however is that the basis with repect to which these mass matrices are realized may not be the weak eigenbasis. The democratic idea somewhat reduces the possible choices for mass matrices and the degrees of freedom seem to have shifted to the choice of the ad-hoc CKM. However the idea of democracy is still present there because in the democratic basis the ”physical” CKM will have its hierarchy smeared. I believe the democratic basis defined in this way, makes the problem easier in an interesting way. Since within the idea of there seems to be a finite amount of reasonnable choices for the ad-hoc CKM.

I must apologize for having omitted references due to the rapid communication nature of this letter.


text:
# A Generalisation of the Cassels and Greub-Reinboldt Inequalities in Inner Product Spaces

## 1. Introduction

The following result was proved by J.W.S. Cassels in 1951 (see Appendix 1 of ).

###### Theorem 1.

Let $`\overline{𝐚}=(a_1,\mathrm{},a_n),`$ $`\overline{𝐛}=(b_1,\mathrm{},b_n)`$ be sequences of positive real numbers and $`\overline{𝐰}=(w_1,\mathrm{},w_n)`$ a sequence of nonnegative real numbers. Suppose that

(1.1)
$$m=\underset{i=\overline{1,n}}{\mathrm{min}}\left\{\frac{a_i}{b_i}\right\}\text{ and }M=\underset{i=\overline{1,n}}{\mathrm{max}}\left\{\frac{a_i}{b_i}\right\}.$$

Then one has the inequality

(1.2)
$$\frac{_{i=1}^nw_ia_i^2_{i=1}^nw_ib_i^2}{\left(_{i=1}^nw_ia_ib_i\right)^2}\frac{\left(m+M\right)^2}{4mM}.$$

The equality holds in (1.2) when $`w_1=\frac{1}{a_1b_1},`$ $`w_n=\frac{1}{a_nb_n},`$ $`w_2=\mathrm{}=w_{n1}=0,`$ $`m=\frac{a_n}{b_1}`$ and $`M=\frac{a_1}{b_n}.`$

If one assumes that $`0<aa_iA<\mathrm{}`$ and $`0<bb_iB<\mathrm{}`$ for each $`i\{1,\mathrm{},n\},`$ then by (2.2) we may obtain Greub-Reinboldt’s inequality

(1.3)
$$\frac{_{i=1}^nw_ia_i^2_{i=1}^nw_ib_i^2}{\left(_{i=1}^nw_ia_ib_i\right)^2}\frac{\left(ab+AB\right)^2}{4abAB}.$$

The following “unweighted” Cassels’ inequality also holds

(1.4)
$$\frac{_{i=1}^na_i^2_{i=1}^nb_i^2}{\left(_{i=1}^na_ib_i\right)^2}\frac{\left(m+M\right)^2}{4mM},$$

provided $`\overline{𝐚}`$ and $`\overline{𝐛}`$ satisfy (1.1). This inequality will produce the well known Pólya-Szegö inequality \[7, pp. 57, 213-114\], \[4, pp. 71-72, 253-255\]:

(1.5)
$$\frac{_{i=1}^na_i^2_{i=1}^nb_i^2}{\left(_{i=1}^na_ib_i\right)^2}\frac{\left(ab+AB\right)^2}{4abAB},$$

provided $`0<aa_iA<\mathrm{}`$ and $`0<bb_iB<\mathrm{}`$ for each $`i\{1,\mathrm{},n\}.`$

In , C.P. Niculescu proved, amongst others, the following generalisation of Cassels’ inequality:

###### Theorem 2.

Let $`E`$ be a vector space endowed with a Hermitian product $`,.`$ Then

(1.6)
$$\frac{\mathrm{R}ex,y}{x,x^{\frac{1}{2}}y,y^{\frac{1}{2}}}\frac{2}{\sqrt{\frac{\omega }{\mathrm{\Omega }}}+\sqrt{\frac{\mathrm{\Omega }}{\omega }}}$$

for every $`x,yE`$ and every $`\omega ,\mathrm{\Omega }>0`$ for which $`\mathrm{R}ex\omega y,x\mathrm{\Omega }y0.`$

For other reverses of the Cauchy-Bunyakovsky-Schwarz, see the references -.

In this paper we obtain a generalisation of (1.6) for complex numbers $`\omega `$ and $`\mathrm{\Omega }`$ for which $`\mathrm{R}e\left(\overline{\omega }\mathrm{\Omega }\right)>0.`$ Applications for isotonic linear functionals, integrals and sequences are also given.

## 2. The Results

The following reverse of Schwarz’s inequality in inner product spaces holds.

###### Theorem 3.

Let $`a,A𝕂`$ $`\left(𝕂=,\right)`$ so that $`\mathrm{R}e\left(\overline{a}A\right)>0.`$ If $`x,yH`$ are such that

(2.1)
$$\mathrm{R}eAyx,xay0,$$

then one has the inequality

(2.2)
$$xy\frac{1}{2}\frac{\mathrm{R}e\left[A\overline{x,y}+\overline{a}x,y\right]}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}\frac{1}{2}\frac{\left|A\right|+\left|a\right|}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}\left|x,y\right|.$$

The constant $`\frac{1}{2}`$ is sharp in both inequalities.

###### Proof.

We have, obviously, that

$$I:=\mathrm{R}eAyx,xay=\mathrm{R}e\left[A\overline{x,y}+\overline{a}x,y\right]x^2\left[\mathrm{R}e\left(\overline{a}A\right)\right]y^2$$

and, thus, by (2.1), one has

$$x^2+\left[\mathrm{R}e\left(\overline{a}A\right)\right]y^2\mathrm{R}e\left[A\overline{x,y}+\overline{a}x,y\right],$$

giving

(2.3)
$$\frac{1}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}x^2+\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}y^2\frac{\mathrm{R}e\left[A\overline{x,y}+\overline{a}x,y\right]}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}.$$

On the other hand, by the elementary inequality

$$\alpha p^2+\frac{1}{\alpha }q^22pq$$

holding for $`p,q0`$ and $`\alpha >0,`$ we deduce

(2.4)
$$2xy\frac{1}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}x^2+\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}y^2.$$

Utilizing (2.3) and (2.4) we deduce the first part of (2.2).

The last part is obvious by the fact that for $`z,`$ $`\left|\mathrm{R}e\left(z\right)\right|\left|z\right|.`$

Now, assume that the first inequality in (2.2) holds with a constant $`c>0,`$ i.e.,

(2.5)
$$xyc\frac{\mathrm{R}e\left[A\overline{x,y}+\overline{a}x,y\right]}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}},$$

where $`a,A,x`$ and $`y`$ satisfy (2.2).

If we choose $`a=A=1,`$ $`y=x0,`$ then obviously (2.2) holds and from (2.5) we may obtain

$$x^22cx^2,$$

giving $`c\frac{1}{2}.`$

The theorem is completely proved.

The following corollary is a natural consequence of the above theorem.

###### Corollary 1.

Let $`m,M>0.`$ If $`x,yH`$ are such that

(2.6)
$$\mathrm{R}eMyx,xmy0,$$

then one has the inequality

(2.7)
$$xy\frac{1}{2}\frac{M+m}{\sqrt{mM}}\mathrm{R}ex,y\frac{1}{2}\frac{M+m}{\sqrt{mM}}\left|x,y\right|.$$

The constant $`\frac{1}{2}`$ is sharp in (2.7).

###### Remark 1.

The inequality (2.7) is equivalent to Niculescu’s inequality (1.6).

The following corollary is also obvious.

###### Corollary 2.

With the assumptions of Corollary 1, we have

(2.8) $`0`$ $`xy\left|x,y\right|xy\mathrm{R}ex,y`$
$`{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}\mathrm{R}ex,y{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}\left|x,y\right|`$
and

(2.9) $`0`$ $`x^2y^2\left|x,y\right|^2x^2y^2\left[\mathrm{R}ex,y\right]^2`$
$`{\displaystyle \frac{\left(Mm\right)^2}{4mM}}\left[\mathrm{R}ex,y\right]^2{\displaystyle \frac{\left(Mm\right)^2}{4mM}}\left|x,y\right|^2.`$
###### Proof.

If we subtract $`\mathrm{R}ex,y0`$ from the first inequality in (2.7), we get

$`xy\mathrm{R}ex,y`$ $`\left({\displaystyle \frac{1}{2}}{\displaystyle \frac{M+m}{\sqrt{mM}}}1\right)\mathrm{R}ex,y`$
$`={\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}\mathrm{R}ex,y`$
which proves the third inequality in (2.8). The other ones are obvious.

Now, if we square the first inequality in (2.7) and then subtract $`\left[\mathrm{R}ex,y\right]^2,`$ we get

$`x^2y^2\left[\mathrm{R}ex,y\right]^2`$ $`\left[{\displaystyle \frac{\left(M+m\right)^2}{4mM}}1\right]\left[\mathrm{R}ex,y\right]^2`$
$`={\displaystyle \frac{\left(Mm\right)^2}{4mM}}\left[\mathrm{R}ex,y\right]^2`$
which proves the third inequality in (2.5). The other ones are obvious.

## 3. Applications for Isotonic Linear Functionals

Let $`F\left(T\right)`$ be an algebra of real functions defined on $`T`$ and $`L`$ a subclass of $`F\left(T\right)`$ satisfying the conditions:

1. $`f,gL`$ implies $`f+gL;`$
2. $`fL,`$ $``$ implies $`\alpha fL.`$

A functional $`A`$ defined on $`L`$ is an isotonic linear functional on $`L`$ provided that

1. $`A\left(\alpha f+\beta g\right)=\alpha A\left(f\right)+\beta A\left(g\right)`$ for all $`\alpha ,\beta `$ and $`f,gL;`$
2. $`fg,`$ that is, $`f\left(t\right)g\left(t\right)`$ for all $`tT,`$ implies $`A\left(f\right)A\left(g\right).`$

The functional $`A`$ is normalised on $`L,`$ provided that $`\mathrm{𝟏}L,`$ i.e., $`\mathrm{𝟏}\left(t\right)=1`$ for all $`tT,`$ implies $`A\left(\mathrm{𝟏}\right)=1.`$

Usual examples of isotonic linear functionals are integrals, sums, etc.

Now, suppose that $`hF\left(T\right),`$ $`h0`$ is given and satisfies the properties that $`fghL,`$ $`fhL,`$ $`ghL`$ for all $`f,gL.`$ For a given isotonic linear functional $`A:L`$ with $`A\left(h\right)>0,`$ define the mapping $`(,)_{A,h}:L\times L`$ by

$$(f,g)_{A,h}:=\frac{A\left(fgh\right)}{A\left(h\right)}.$$

This functional satisfies the following properties:

1. $`(f,f)_{A,h}0`$ for all $`fL;`$
2. $`(\alpha f+\beta g,k)_{A,h}=\alpha (f,k)_{A,h}+\beta (g,k)_{A,h}`$ for all $`f,g,kL`$ and $`\alpha ,\beta `$;
3. $`(f,g)_{A,h}=(g,f)_{A,h}`$ for all $`f,gL.`$

The following proposition holds.

###### Proposition 1.

Let $`f,g,hF\left(T\right)`$ be such that $`fghL,`$ $`f^2hL,`$ $`g^2hL.`$ If $`m,M>0`$ are such that

(3.1)
$$mgfMg\text{ on }F\left(T\right),$$

then for any isotonic linear functional $`A:L`$ with $`A\left(h\right)>0,`$ we have the inequality

(3.2)
$$1\frac{A\left(f^2h\right)A\left(g^2h\right)}{A^2\left(fgh\right)}\frac{\left(M+m\right)^2}{4mM}.$$

The constant $`\frac{1}{4}`$ in (3.2) is sharp.

###### Proof.

We observe that

$$(Mgf,fmg)_{A,h}=A\left[h\left(Mgf\right)\left(fmg\right)\right]0.$$

Applying Corollary 1 for $`(,)_{A,L}`$ we get

$$1\frac{(f,f)_{A,h}(g,g)_{A,h}}{(f,g)_{A,h}^2}\frac{\left(M+m\right)^2}{4mM},$$

which is clearly equivalent to (3.2).

The following additive versions of (3.2) also hold.

###### Corollary 3.

With the assumption in Proposition 1, one has

(3.3) $`0`$ $`\left[A\left(f^2h\right)A\left(g^2h\right)\right]^{\frac{1}{2}}A\left(hfg\right)`$
$`{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}A\left(hfg\right)`$
and

(3.4) $`0`$ $`A\left(f^2h\right)A\left(g^2h\right)A^2\left(fgh\right)`$
(3.5) $`{\displaystyle \frac{\left(Mm\right)^2}{4mM}}A^2\left(fgh\right).`$
###### Remark 2.

The condition (3.1) may be replaced with the weaker assumption

(3.6)
$$(Mgf,fmg)_{A,h}0.$$

###### Remark 3.

With the assumption (3.1) or (3.6) and if $`f,gF\left(T\right)`$ with $`fg,f^2,g^2L,`$ then one has the inequality

(3.7)
$$1\frac{A\left(f^2\right)A\left(g^2\right)}{A^2\left(fg\right)}\frac{\left(M+m\right)^2}{4mM},$$

(3.8) $`0`$ $`\left[A\left(f^2\right)A\left(g^2\right)\right]^{\frac{1}{2}}A\left(fg\right)`$
$`{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}A\left(fg\right)`$
and

(3.9)
$$0A\left(f^2\right)A\left(g^2\right)A^2\left(fg\right)\frac{\left(Mm\right)^2}{4mM}A^2\left(fg\right).$$

## 4. Applications for Integrals

Let $`(\mathrm{\Omega },\mathrm{\Sigma },\mu )`$ be a measure space consisting of a set $`\mathrm{\Omega },`$ a $`\sigma `$algebra $`\mathrm{\Sigma }`$ of subsets of $`\mathrm{\Omega }`$ and a countably additive and positive measure on $`\mathrm{\Sigma }`$ with values in $`\left\{\mathrm{}\right\}.`$

Denote by $`L_\rho ^2(\mathrm{\Omega },𝕂)`$ the Hilbert space of all $`𝕂`$-valued functions $`f`$ defined on $`\mathrm{\Omega }`$ that are $`2\rho `$integrable on $`\mathrm{\Omega },`$ i.e., $`_\mathrm{\Omega }\rho \left(t\right)\left|f\left(s\right)\right|^2𝑑\mu \left(s\right)<\mathrm{},`$ where $`\rho :\mathrm{\Omega }[0,\mathrm{})`$ is a measurable function on $`\mathrm{\Omega }.`$

The following proposition contains a counterpart of the weighted Cauchy-Bunyakovsky-Schwarz’s integral inequality.

###### Proposition 2.

Let $`A,a𝕂`$ $`\left(𝕂=,\right)`$ with $`\mathrm{R}e\left(\overline{a}A\right)>0`$ and $`f,gL_\rho ^2(\mathrm{\Omega },𝕂).`$ If

(4.1)
$$_\mathrm{\Omega }\mathrm{R}e\left[\left(Ag\left(s\right)f\left(s\right)\right)\left(\overline{f\left(s\right)}\overline{a}\text{ }\overline{g}\left(s\right)\right)\right]\rho \left(s\right)d\mu \left(s\right)0,$$

then one has the inequality

(4.2) $`\left[{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|f\left(s\right)\right|^2𝑑\mu \left(s\right){\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|g\left(s\right)\right|^2𝑑\mu \left(s\right)\right]^{\frac{1}{2}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{_\mathrm{\Omega }\rho \left(s\right)\mathrm{R}e\left[A\overline{f\left(s\right)}g\left(s\right)+\overline{a}f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{\left|A\right|+\left|a\right|}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}\left|{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)f\left(s\right)\overline{g\left(s\right)}𝑑\mu \left(s\right)\right|.`$
The constant $`\frac{1}{2}`$ is sharp in (4.2).

###### Proof.

Follows by Theorem 3 applied for the inner product $`,_\rho :=L_\rho ^2(\mathrm{\Omega },𝕂)\times L_\rho ^2(\mathrm{\Omega },𝕂)𝕂`$,

$$f,g:=_\mathrm{\Omega }\rho \left(s\right)f\left(s\right)\overline{g\left(s\right)}𝑑\mu \left(s\right).$$

###### Remark 4.

A sufficient condition for (4.1) to hold is

(4.3)
$$\mathrm{R}e\left[\left(Ag\left(s\right)f\left(s\right)\right)\left(\overline{f\left(s\right)}\overline{a}\overline{g\left(s\right)}\right)\right]0\text{ for }\mu \text{-a.e. }s\mathrm{\Omega }.$$

In the particular case $`\rho =1,`$ we have the following result.

###### Corollary 4.

Let $`a,A𝕂`$ $`\left(𝕂=,\right)`$ with $`\mathrm{R}e\left(\overline{a}A\right)>0`$ and $`f,gL^2(\mathrm{\Omega },𝕂).`$ If

(4.4)
$$_\mathrm{\Omega }\mathrm{R}e\left[\left(Ag\left(s\right)f\left(s\right)\right)\left(\overline{f\left(s\right)}\overline{a}\overline{g\left(s\right)}\right)\right]d\mu \left(s\right)0,$$

then one has the inequality

(4.5) $`\left[{\displaystyle _\mathrm{\Omega }}\left|f\left(s\right)\right|^2𝑑\mu \left(s\right){\displaystyle _\mathrm{\Omega }}\left|g\left(s\right)\right|^2𝑑\mu \left(s\right)\right]^{\frac{1}{2}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{_\mathrm{\Omega }\mathrm{R}e\left[A\overline{f\left(s\right)}g\left(s\right)+\overline{a}f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{\left|A\right|+\left|a\right|}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}\left|{\displaystyle _\mathrm{\Omega }}f\left(s\right)\overline{g\left(s\right)}𝑑\mu \left(s\right)\right|.`$
###### Remark 5.

If $`𝕂=,`$ then a sufficient condition for either (4.1) or (4.4) to hold is

(4.6)
$$ag\left(s\right)f\left(s\right)Ag\left(s\right)\text{ for }\mu \text{-a.e. }s\mathrm{\Omega },$$

where, in this case, $`a,A`$ with $`A>a>0.`$

When $`a,A`$ are real positive constants, then the following proposition holds.

###### Proposition 3.

Let $`m,M>0.`$ If $`f,gL_\rho ^2(\mathrm{\Omega },𝕂)`$ such that

(4.7)
$$_\mathrm{\Omega }\rho \left(s\right)\mathrm{R}e\left[\left(Mg\left(s\right)f\left(s\right)\right)\left(\overline{f\left(s\right)}m\overline{g}\left(s\right)\right)\right]d\mu \left(s\right)0$$

then one has the inequality

(4.8)
$$\begin{array}{c}\left[_\mathrm{\Omega }\rho \left(s\right)\left|f\left(s\right)\right|^2𝑑\mu \left(s\right)_\mathrm{\Omega }\rho \left(s\right)\left|g\left(s\right)\right|^2𝑑\mu \left(s\right)\right]^{\frac{1}{2}}\hfill \\ \hfill \frac{1}{2}\frac{M+m}{\sqrt{mM}}_\mathrm{\Omega }\rho \left(s\right)\mathrm{R}e\left[f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right).\end{array}$$

The proof follows by Corollary 1 applied for the inner product

$$f,g_\rho :=_\mathrm{\Omega }\rho \left(s\right)f\left(s\right)\overline{g\left(s\right)}𝑑\mu \left(s\right).$$

The following additive versions also hold.

###### Corollary 5.

With the assumptions in Proposition 3, one has the inequalities

(4.9) $`0`$ $`\left[{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|f\left(s\right)\right|^2𝑑\mu \left(s\right){\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|g\left(s\right)\right|^2𝑑\mu \left(s\right)\right]^{\frac{1}{2}}`$
$`{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\mathrm{R}e\left[f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)`$
$`{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\mathrm{R}e\left[f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)`$
and

(4.10) $`0`$ $`{\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|f\left(s\right)\right|^2𝑑\mu \left(s\right){\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\left|g\left(s\right)\right|^2𝑑\mu \left(s\right)`$
$`\left({\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\mathrm{R}e\left[f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)\right)^2`$
$`{\displaystyle \frac{\left(Mm\right)^2}{4mM}}\left({\displaystyle _\mathrm{\Omega }}\rho \left(s\right)\mathrm{R}e\left[f\left(s\right)\overline{g\left(s\right)}\right]d\mu \left(s\right)\right)^2.`$
###### Remark 6.

If $`𝕂=`$, a sufficient condition for (4.1) to hold is

(4.11)
$$mg\left(s\right)f\left(s\right)Mg\left(s\right)\text{ for }\mu \text{-a.e. }s\mathrm{\Omega },$$

where $`M>m>0.`$

## 5. Applications for Sequences

For a given sequence $`\left(w_i\right)_i`$ of nonnegative real numbers, consider the Hilbert space $`\mathrm{}_w^2\left(𝕂\right),`$ $`\left(𝕂=,\right),`$ where

(5.1)
$$\mathrm{}_w^2\left(𝕂\right):=\left\{\overline{x}=\left(x_i\right)_i𝕂\right|\underset{i=0}{\overset{\mathrm{}}{}}w_i\left|x_i\right|^2<\mathrm{}\}.$$

The following proposition that provides a counterpart of the weighted Cauchy-Bunyakovsky-Schwarz inequality for complex numbers holds.

###### Proposition 4.

Let $`a,A𝕂`$ with $`\mathrm{R}e\left(\overline{a}A\right)>0`$ and $`\overline{x},\overline{y}\mathrm{}_w^2\left(𝕂\right).`$ If

(5.2)
$$\underset{i=0}{\overset{\mathrm{}}{}}w_i\mathrm{R}e\left[\left(Ay_ix_i\right)\left(\overline{x_i}\overline{a}\overline{y_i}\right)\right]0,$$

then one has the inequality

(5.3) $`\left[{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|x_i\right|^2{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|y_i\right|^2\right]^{\frac{1}{2}}`$ $`{\displaystyle \frac{1}{2}}{\displaystyle \frac{_{i=0}^{\mathrm{}}w_i\mathrm{R}e\left[A\overline{x_i}y_i+\overline{a}x_i\overline{y_i}\right]}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{\left|A\right|+\left|a\right|}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}\left|{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_ix_i\overline{y_i}\right|.`$
The constant $`\frac{1}{2}`$ is sharp in (5.3).

###### Proof.

Follows by Theorem 3 applied for the inner product $`,:\mathrm{}_w^2\left(𝕂\right)\times \mathrm{}_w^2\left(𝕂\right)𝕂`$,

$$\overline{x},\overline{y}_w:=\underset{i=0}{\overset{\mathrm{}}{}}w_ix_i\overline{y_i}.$$

###### Remark 7.

A sufficient condition for (5.2) to hold is

(5.4)
$$\mathrm{R}e\left[\left(Ay_ix_i\right)\left(\overline{x_i}\overline{a}\overline{y_i}\right)\right]0\text{ for all }i.$$

In the particular case $`\rho =1,`$ we have the following result.

###### Corollary 6.

Let $`a,A𝕂`$ with $`\mathrm{R}e\left(\overline{a}A\right)>0`$ and $`\overline{x},\overline{y}\mathrm{}^2\left(𝕂\right).`$ If

(5.5)
$$\underset{i=0}{\overset{\mathrm{}}{}}\mathrm{R}e\left[\left(Ay_ix_i\right)\left(\overline{x_i}\overline{a}\overline{y_i}\right)\right]0,$$

then one has the inequality

(5.6) $`\left[{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}\left|x_i\right|^2{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}\left|y_i\right|^2\right]^{\frac{1}{2}}`$ $`{\displaystyle \frac{1}{2}}{\displaystyle \frac{_{i=0}^{\mathrm{}}\mathrm{R}e\left[A\overline{x_i}y_i+\overline{a}x_i\overline{y_i}\right]}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}`$
$`{\displaystyle \frac{1}{2}}{\displaystyle \frac{\left|A\right|+\left|a\right|}{\left[\mathrm{R}e\left(\overline{a}A\right)\right]^{\frac{1}{2}}}}\left|{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}x_i\overline{y_i}\right|.`$
###### Remark 8.

If $`𝕂=`$, then a sufficient condition for either (5.1) or (5.4) to hold is

(5.7)
$$ay_ix_iAy_i\text{ for each }i\{1,\mathrm{},n\},$$

where, in this case, $`a,A`$ with $`aA>0.`$

When the constants are positive, then the following proposition also holds.

###### Proposition 5.

Let $`m,M>0.`$ If $`\overline{x},\overline{y}\mathrm{}_w^2\left(𝕂\right)`$ such that

(5.8)
$$\underset{i=0}{\overset{\mathrm{}}{}}w_i\mathrm{R}e\left[\left(My_ix_i\right)\left(\overline{x_i}m\overline{y_i}\right)\right]0,$$

then one has the inequality

(5.9)
$$\left[\underset{i=0}{\overset{\mathrm{}}{}}w_i\left|x_i\right|^2\underset{i=0}{\overset{\mathrm{}}{}}w_i\left|y_i\right|^2\right]^{\frac{1}{2}}\frac{1}{2}\frac{M+m}{\sqrt{mM}}\underset{i=0}{\overset{\mathrm{}}{}}w_i\mathrm{R}e\left(x_i\overline{y_i}\right).$$

The proof follows by Corollary 1 applied for the inner product

$$\overline{x},\overline{y}_w:=\underset{i=0}{\overset{\mathrm{}}{}}w_ix_i,\overline{y_i}.$$

The following additive version also holds.

###### Corollary 7.

With the assumptions in Proposition 5, one has the inequalities

(5.10) $`0`$ $`\left[{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|x_i\right|^2{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|y_i\right|^2\right]^{\frac{1}{2}}{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\mathrm{R}e\left(x_i\overline{y_i}\right)`$
$`{\displaystyle \frac{\left(\sqrt{M}\sqrt{m}\right)^2}{2\sqrt{mM}}}{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\mathrm{R}e\left(x_i\overline{y_i}\right)`$
and

(5.11) $`0`$ $`{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|x_i\right|^2{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\left|y_i\right|^2\left[{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\mathrm{R}e\left(x_i\overline{y_i}\right)\right]^2`$
$`{\displaystyle \frac{\left(Mm\right)^2}{4mM}}\left[{\displaystyle \underset{i=0}{\overset{\mathrm{}}{}}}w_i\mathrm{R}e\left(x_i\overline{y_i}\right)\right]^2.`$
###### Remark 9.

If $`𝕂=`$, a sufficient condition for (5.8) to hold is

(5.12)
$$my_ix_iMy_i\text{ for each }i,$$

where $`M>m>0.`$


text:
# SCRAM: Software configuration and management for the LHC Computing Grid project.

## I Configuration management concepts and their realization in SCRAM

Configuration management with SCRAM is based on the following concepts:

* PBS
* Product specification
* Product versioning
* Configuration definition and versioning
* Product-wise configuration selection
* Assembly break-down.

Here the PBS is the set of products, tools, etc. that are used in all software systems. These may be compilers like gcc, external packages like zlib or root, or experiment owned software like the reconstruction code.

SCRAM product specifications are expected to be collected in a repository of their own, that enables versioning, and distributed access. There is exactly one specification file per product, which gives for each version of the product a complete description the product and the environment, compile time and run time, it needs for being used. This can relate to include paths, library paths, runtime settings, locations for graphics resources, license file-names, etc..

Product versioning is not done by SCRAM. It relies in this respect on a standard versioning system, like cvs, or simply the version numbers of external components, as delivered.

The configuration is then defined as an inclusive and consistent set of product specifications and versions, that are referred to in a single file, the configuration file. This configuration file in turn is versioned using a standard versioning system, like cvs. It can be referred to by name and version from any SCRAM managed software development project in the project’s ’Requirements’ file. To realize the assembly break down, each SCRAM managed project then selects from the configuration, by name, the tools/products it depends on. The version numbers of these tools will then be taken as specified in the selected version of the configuration file. The requirements document itself is parts of a project’s release.

## II Functionality and design

The principal goal of SCRAM is to provide developers located in different institutions and using differing operational environments with an easy way to use consistent development environments. By doing this, SCRAM enables massively parallel and distributed software development in a multi-project environment. It does this by applying strict configuration management. In addition, it provides a build system, and a mechanism for source code distribution.

SCRAM is mapping the application’s requirements onto a given target operational environment. It extracts information on the target system, and maps the configuration requirements of each product used onto actually installed components in the local operational environment.

The SCRAM managed project has three areas of concern. Source code distribution which is governed by the BootStrapFiles, configuration management governed by the Requirements documents, and the builds, governed by the BuildFiles.

SCRAM itself is written in object oriented perl, for easy installation.

### II.1 SCRAM documents and parsing

All SCRAM documents are written in a XML style language, and SCRAM contains the ActiveDoc parser, to handle these documents.

Each document is typed and versioned in turn, like in

```
<doc type=a:b version=2.1>

```

Functions may then map any document tag onto any object method. Multi-parsing is enabled, hence documents can refer to other documents. The syntax is based on a URL retrieval mechanism. Currently cvs: and file: types are supported, and an interface for plugging in new types is provided. Documents can be inlined using

```
<inline url="MyDocumentToInline">.

```

A cache mechanism for already fetched documents optimizes access and retrieval times.

The document classes available are ActiveDoc, SimpleURLDoc, and SimpleDoc. Here SimpleDoc is the base-class, has the parsing kernel, enables multi-parsing, and grouping of tags. SimpleURLDoc adds URL retrieval mechanisms, document versioning, as well as the URL cache. ActiveDoc finally adds preprocessing and type activation including the object store.

### II.2 Client project installation

The mechanism for installation of a SCRAM managed product is described in its BootStrapFile. This file is part of any release of a SCRAM managed project. A client will start the installation procedure by downloading the projects BootStrapFile through WWW. SCRAM then assembles the components described in the BootStrap document into a central installation area. In case a Requirements document is specified in the released project, SCRAM attempts to find the selected products in the client’s operational environment. If provided, SCRAM uses the specification in a site description file to achieve this. For products that cannot be automatically mapped completely, the installer will be asked to provide the information necessary to conclude the resource mapping on the command line. Depending on the nature of the project, the installer then may have to issue a build command, scram build. Once the build was successful and the installation was verified, issuing the scram install command will make the central installation available for dependent work by developers and users. It is now ready for use.

### II.3 Requirement and product specification documents

The product specification documents serve the purpose to make it such that users and developers do not need to know about the environment needed by the application and development areas. One of the more complicated real-life examples of a tool description file is given below:

```
<doc type=BuildSystem::ToolDoc version=1.0>
<Tool name=Boost version=1.28.0>
<info url=http://www.boost.org></info>
<Lib name=boost_thread>
<Client>
<Environment name=BOOST_BASE>
  The top of the Boost distribution.
</Environment>
<Environment name=LIBDIR type=lib></Environment>
<Environment name=INCLUDE></Environment>
</Client>
<External ref=sockets version=1.0>
We need the sockets libs
</External>
<Environment name=LD_LIBRARY_PATH value=$LIBDIR
             type=Runtime_path></Environment>
</Tool>
<Tool name=Boost version=1.29.0>
<info url=http://www.boost.org></info>
<Lib name=boost_thread>
<Client>
<Environment name=BOOST_BASE>
The top of the Boost distribution.
</Environment>
<Environment name=LIBDIR type=lib></Environment>
<Environment name=INCLUDE></Environment>
</Client>
<External ref=sockets version=1.0>
We need the sockets libs
</External>
<Environment name=LD_LIBRARY_PATH value=$LIBDIR
             type=Runtime_path></Environment>
</Tool>
<Tool name=Boost version=1.30.0>
<info url=http://www.boost.org></info>
<Lib name=boost_thread>
<Client>
<Environment name=BOOST_BASE>
The top of the Boost distribution.
</Environment>
<Environment name=LIBDIR type=lib></Environment>
<Environment name=INCLUDE></Environment>
</Client>
<External ref=sockets version=1.0>
We need the sockets libs
</External>
<Environment name=LD_LIBRARY_PATH value=$LIBDIR
             type=Runtime_path></Environment>
</Tool>

```

This example specifies the product boost for a set of versions of this product. It specifies for each version the name of the product, where to find product information, and the names of the product’s libraries. It enables search for library and include paths, and specifies the external dependencies of the product, in this case the sockets library.

One product specification file is maintained per product, ideally by the author or an expert of this product. Users and developers in turn have no need to know any of the details of the product’s implementation and installation to be able to use it.

The product specification files will be collected into a versioned configuration file, using require tags. Below a snippet of such a configuration file:

```
...
<Architecture name=SunOS__5>
  <require name=f77  version=4.2ΨΨurl="cvs:?module=SCRAMToolBox/Fortran/SunF77">
  </require>
  <require name=CC   version=5.4ΨΨurl="cvs:?module=SCRAMToolBox//CXX/SunCC">
  </require>
</Architecture>
<Architecture name=Linux__2.4>
  <require name=gcc3 version=3.2ΨΨurl="cvs:?module=SCRAMToolBox/CXX/gcc3">
  </require>
  <require name=gcc  version=2.95.2Ψurl="cvs:?module=SCRAMToolBox/CXX/gcc">
  </require>
  <require name=g77  version=0.5.24Ψurl="cvs:?module=SCRAMToolBox/Fortran/g77">
  </require>
  <require name=icc  version=7.0Ψ        url="cvs:?module=SCRAMToolBox/CXX/icc">
  </require>
</Architecture>
  <require name=LHCxx  version=5.0.3Ψurl="cvs:?module=SCRAMToolBox/LHCxx/LHCxx">
  </require>
  <require name=Qt     version=3.1.2Ψurl="cvs:?module=SCRAMToolBox/LHCxx/Qt">
  </require>
  <require name=CLHEP  version=1.8.0.0Ψurl="cvs:?module=SCRAMToolBox/LHCxx/CLHEP">
  </require>
...

```

It shows how the various products with concrete versions are grouped together into one configuration. Dependencies on the operational environment, like in the case of compilers, are taken into account through Architecture tags.

Any SCRAM managed project will have a Requirements document, that specifies the configuration and configuration version it wishes to use. In this document, the project will then select by name the products used. An example snippet below:

```
<doc type=BuildSystem::Requirements version=2.0>
<base url="cvs://cmscvs.cern.ch/.../SCRAMToolBox
       ?auth=...&user=...&version=CMS_68_2">
<include url="cvs:?module=.../CMSconfiguration">
<Architecture name=SunOS__5.8>
<select name=CC>
<select name=f77>
</Architecture>
<Architecture name=Linux__2.4>
<select name=gcc3>
<select name=g77gcc3>
</Architecture>
<select name=COBRA>
<select name=IGUANA>
<select name=CMSToolBox>
<select name=Geometry>
<select name=AIDA>
<select name=AIDA_Dev>
<select name=AIDA_XMLStore>
<select name=AIDA_AnalysisFactory_native>
<select name=AIDA_Tree_native>

```

Again Architecture tags are used to resolve dependencies on the operational environment. Since the version selection is done centrally in the configuration, a multi-project environment is kept consistent in the most natural manner.

### II.4 The distributed development model

SCRAM assumes a work-model, in which development is done in multiple projects, and for each project on multiple, internationally distributed sites. It is assuming a rather rapid release cycle, and that an installation of the project versions to be further developed is centrally available at each site. Developers will have a local development area, drawing resources from this central installation, while only the part that a developer wishes to change is kept locally. It is the central installation that maps the projects requirements onto the local system’s resources, contains a complete set of source code and build products, provides for the definition of the environment associated to the project, has the URL and object cache, but is still self-contained, and hence movable without breaking. It also defines the context of all functions of SCRAM.

The developer areas are linked to the central installation, and use all elements of this installation that were not changed by the developer, resulting in a significant saving of both time and computing resources.

Easy look-up of available central installations is provided, and the context of the development area is defined by the associated installation. Changing the development area, using cd, will result in a change of the environment. This enables easy and transparent use of multiple releases and projects by an individual developer.

At the time of writing, the development area is tightly controlled by the build system.

### II.5 The build system

At the time of writing, the build system is undergoing major changes. A description of these is deferred to a later publication.

## III The users view

### III.1 Development areas and central installations

The user of SCRAM is provided with an isolated and well defined environment so he can focus on development of code, while the environment is defined by the central installation he bases his work on. The user will find the available installations by using the scram list command as in the following:

```
scram list ORCA

Listing installed projects....

------------------------------------
| Project  | Version  |  Location  |
------------------------------------
...
ORCA 7_1_2 --> /afs/cern.ch/.../ORCA_7_1_2
ORCA 7_1_3 --> /afs/cern.ch/.../ORCA_7_1_3
...
Projects available for platform >> Linux__2.4 <<

```

He will then want to create the desired developers area using the scram project command, like in:

```
scram project ORCA 7_1_3

```

This will create a development area that refers to the central installation of a project called ORCA with version 7\_1\_3.

The structure of the development area is such that it contains a src area to be used by the user for changing source code, a config area that contains the information on the configuration, lib and bin areas for build products, a logs area for log file storage, a tmp area that is the working area of the build system, and a .SCRAM area, which is used by SCRAM for administration files. The real working area hence is the src directory.

### III.2 Product description management

As described earlier, all product descriptions live in a repository. If a developer wishes to find out what products he depends on, he can issue the scram tool list command to query the installation. This will yield the complete list of products used, with their version in the configuration, and the version used by the development area. Normally, the two will be identical.

```
scram tool list

Tool list for location .../ORCA_7_1_2
++++++++++++++++++++++++++++++++++++++++++++++++++
...
 gcc                  2.95.2     (default=2.95.2)
 g77                  0.5.24     (default=0.5.24)
 qt                   3.0.5      (default=3.0.5)
 clhep                1.8.0.0    (default=1.8.0.0)
 heputilities         0.7.1.1    (default=0.7.1.1)
 gemini               1.3.0.3    (default=1.3.0.3)
 openinventor         3.1.1      (default=3.1.1)
...

```

If a user wishes to use a product not in the configuration, or wishes to change a products version, he can issue the scram setup command, like in

```
scram setup htl 1.5 cvs://...&module=HTL

```

SCRAM will in turn try to find the specified product/version combination on the developer’s system, may ask questions on the command line to obtain additional information, may provide hints for installation of the product, etc..

To find out details on the environment a particular product has, the scram tool info command can be used. It will simply retrieve and display the information specified in the product specification for the version of the product in current use.

Developing product specifications is done by editing the specification files, and running scram setup to initiate the changes for the local development area. Normally this should be done in the context of configuration management. To make local changes useful outside the individual developer’s area, they need to be made available such that the URL access mechanism can be used with one of the supported tags.

### III.3 The environment

The runtime environment is set up by entering the directory structure of the development area, and issuing the command eval ‘scram runtime -csh‘. This will set the environment for the current development area consistent with the requirements of the corresponding central installation. It also will roll back any environment settings that may stem from different development areas this user works on, so switching areas is easy.

In case different applications built in the same project context require different runtime settings, these can be described in an application environment file. SCRAM will read this file, and adjust the environment accordingly.

## IV Part of a component system

SCRAM was conceived to be part of a component system for process support, and hence defines interfaces to other parts of a general process support infrastructure. The processes and process elements considered are code management, change management, binary distribution, dependency analysis and QA, software integration, and validation and verification.

## V Underlying technology

With the decision of building SCRAM as a scripted instrument, the requirements for external products have been kept to a strict minimum. The exhaustive list of these products is perl, a make tool, and a shell.

###### Acknowledgements.

The authors wish to thank CERN for their support.


text:
# Van der Waals Density Functional for Layered Structures

thanks: To whom correspondence should be addressed; E-mail: lundqvist@fy.chalmers.se. (August 6, 2003)

## Abstract

To understand sparse systems we must account for both strong local atom bonds and weak nonlocal van der Waals forces between atoms separated by empty space. A fully nonlocal functional form \[H. Rydberg, B.I. Lundqvist, D.C. Langreth, and M. Dion, Phys. Rev. B 62, 6997 (2000)\] of density-functional theory (DFT) is applied here to the layered systems graphite, boron nitride, and molybdenum sulfide to compute bond lengths, binding energies, and compressibilities. These key examples show that the DFT with the generalized-gradient approximation does not apply for calculating properties of sparse matter, while use of the fully nonlocal version appears to be one way to proceed.

Calculations of structure and other properties of sparse systems must account for both strong local atom bonds and weak nonlocal van der Waals (vdW) forces between atoms separated by empty space. Present methods are unable to describe the true interactions of sparse systems, abundant among materials and molecules. Key systems, like graphite, BN, and MoS2, have layered structures. While today’s standard tool, density-functional theory (DFT), has broad application, the common local (LDA) and semilocal density approximations (GGA) PW91 ; PBE ; ZhYa98 ; RPBE  for exchange and correlation, $`E_{\text{xc}}[n]`$, fail to describe the interactions at sparse electron densities. Here we show that the recently proposed density functional RyLuLaDi00  with nonlocal correlations, $`E_\text{c}^{\text{nl}}[n]`$, gives separations, binding energies, and compressibilities of these layered systems in fair agreement with experiment. This planar case bears on the development of vdW density functionals for general geometries RyThesis ; DiRyLuLa03 , as do asymptotic vdW functionals everything .

Figure 1 with its ‘inner surfaces’ defines the problem: voids of ultra-low density, across which electrodynamics leads to vdW coupling. This coupling depends on the polarization properties of the layers themselves, and not on small regions of density overlap between the layers, excluding proper account in LDA or GGA. For large interplanar separation $`d`$ the vdW interaction energy between planes behaves as $`c_4/d^4`$, while LDA or GGA necessarily predicts an exponential falloff. Layers rolled up to form two (i) nanotubes with parallel axes a distance $`l`$ apart interact as $`c_5/l^5`$, or (ii) balls (e.g., C60), a distance $`r`$ apart, as $`c_6/r^6`$. If by fluke an LDA or GGA were to give the correct equilibrium for one shape, it would necessarily fail for the others. The simple expedient of adding the standard asymptotic vdW energies as corrections to the correlation energy of LDA or GGA also fails. The true vdW interaction between two close sheets must be (i) substantially stronger (Fig. 1), (ii) seamless, and (iii) saturate as $`d`$ shrinks (Fig. 2).

Like earlier work directly calculating nonlocal correlations between two jellium slabs DoWa99 , the vdW density functional (vdW-DF) theory RyLuLaDi00  used here exploits assumed planar symmetry. It divides the correlation energy functional into two pieces, $`E_\text{c}[n]=E_\text{c}^0[n]+E_\text{c}^{\text{nl}}[n]`$, where $`E_\text{c}^{\text{nl}}[n]`$ is defined to include the longest ranged or most nonlocal terms that give the vdW interaction and to approach zero in the limit of a slowly varying density. The term $`E_\mathrm{c}^0[n]`$ is also nonlocal, but approaches the LDA in this limit. The two terms are approximated differently. Here the LDA is used for $`E_\text{c}^0[n]`$, as the LDA should be much more accurate with the principal longest range terms separated off. Ultimately we plan to derive a gradient or GGA expansion appropriate to $`E_\text{c}^0[n]`$, but the resulting corrections are expected to be small. Thus we use

$$E_\text{c}[n]E_\text{c}^{\text{LDA}}[n]+E_\text{c}^{\text{nl}}[n].$$
(1)
Long range terms are less sensitive to details of the system’s dielectric response. Thus very simple approximations for the dielectric function are made for $`E_\text{c}^{\text{nl}}[n]`$. We care to make the polarization properties of a single layer come out reasonably.

For systems with planar symmetry, the predominant component of the nonlocal correlation energy $`E_\text{c}^{\text{nl}}`$ giving the vdW forces can be determined simply by comparing the solutions of the Poisson equation $`(ϵ\mathrm{\Phi })=0`$ and the Laplace equation $`^2\mathrm{\Phi }=0`$ RyLuLaDi00 . The crux of the approximation is the use of a simple plasmon-pole model for the dielectric function,

$$ϵ_k(z,iu)=1+\frac{\omega _\mathrm{p}^2(z)}{u^2+(v_\mathrm{F}(z)q_k)^2/3+q_k^4/4},$$
(2)
where $`\omega _\mathrm{p}^2(z)=4\pi n(z)e^2/m`$, and $`mv_\mathrm{F}(z)=(3\pi ^2n(z))^{1/3}`$ are functions of the local density $`n(z)`$. The 2D wave vector perpendicular to the $`z`$ direction is $`𝐤`$, $`iu`$ is the imaginary frequency and $`q_k^2=k^2+q_{}^2`$ mimicks the 3D wave vector, with the $`z`$ direction accounted for by the $`n(z)`$ dependence and $`q_{}`$ taken as a constant.

Our scheme, applied to jellium surfaces in Ref. RyLuLaDi00, , is used here for layered systems, for simplicity a two-layered system (e.g., two parallel graphene sheets) arranged perpendicular to the $`z`$ axis, at positions $`z=0`$ and $`z=d`$, respectively. The first step is to calculate the density in DFT with a suitable approximation, which we take to be an appropriate flavor of the GGA, and to average it in the lateral direction to yield $`n(z)`$. The next two steps represent the key to the success of our approximation. First one calculates from first principles the perpendicular static polarizability $`\alpha `$ of a single layer of the material (a graphene layer in this example) in the ground-state DFT scheme with the above GGA flavor. Then one fixes the constant $`q_{}`$ so that dielectric model (2) gives precisely the same polarizability, that is

$$\alpha =\frac{1}{4\pi }𝑑z\left[1\frac{1}{ϵ_0(z,0)}\right].$$
(3)
This step mitigates the errors introduced both by the lateral averaging and the dielectric model. The leading vdW interaction is proportional to an integral over the square of the dynamic polarizabilities. Previous work in the asymptotic limit everything  shows that simple, properly scaled dielectric functions giving the correct static polarizabilities form good approximations to the dynamic ones, hence giving accurate vdW interactions.

The correlation energy can be calculated from the charge response couplingconstantintegration . With planar symmetry only the response to an arbitrarily charged sheet $`\rho \mathrm{exp}(i𝐤𝐫)\delta (zz_{})`$ placed at an offset $`z_{}`$ ($`z_{}0`$) from one end of the sample needs to be calculated. Integrating Poisson’s equation with $`ϵ`$ as in (2) one finds the $`z`$ component of the electric field $`E_z(z_+)`$ at $`z=z_+d`$. Then $`E_\mathrm{c}^{\text{nl}}`$ is given by RyLuLaDi00

$$E_c^{\text{nl}}=A_0^{\mathrm{}}\frac{du}{2\pi }\frac{d^2k}{(2\pi )^2}\mathrm{ln}\frac{E_z(z_+)}{E_z^0(z_+)},$$
(4)
where $`A`$ is the lateral area and $`E_z^0(z_+)`$ is the electric field component from the charge sheet at $`z=z_{}`$ in the absence of the sample. In Eq. (4) the spatial dependences of the two $`E`$’s cancel in the ratio, leaving only the $`k`$ dependence. For each of the bulk solids considered here we apply this method to 32 and 30 layer slabs to give, by subtraction, a well converged per layer value of $`E_\mathrm{c}^{\mathrm{nl}}`$.

The approximation for the exchange energy functional $`E_\mathrm{x}[n]`$ should be consistent with our approximation for $`E_\mathrm{c}^0[n]`$, that is a local or semilocal one. We use a version that best approximates exact density functional exchange, namely Zhang and Yang’s ZhYa98  (ZY) “revPBE” exchange functional $`E_\text{x}^{\text{ZY}}[n]`$, where the parameter controlling the large gradient limit in the PBE exchange functional PBE  is fitted to exact density-functional exchange calculations. Unlike exchange ScolesPlus  in PW91 PW91 , PBE PBE , and RPBE RPBE , $`E_\text{x}^{\text{ZY}}`$ shows no tendency to bind any of the vdW systems we have tried it on, unless the vdW correlation is actually included in the calculation. We thus take

$$E_{\mathrm{xc}}[n]=E_\text{x}^{\text{ZY}}[n]+E_\text{c}^{\text{LDA}}[n]+E_\text{c}^{\text{nl}}[n].$$
(5)
The first two terms form an important and recommended starting point for testing nonlocal vdW functionals. They assure a vdW attraction that actually comes from terms that in principle are capable of giving it.

The GGA is used in order to have a good account of strong valence bonds and densities of individual layers, and the above scheme is implemented by self-consistently calculating the energy $`E^{\text{GGA}}`$ and density $`n^{\text{GGA}}`$, typically in the revPBE flavor of GGA. The total energy, as a function of the lattice parameters, is then calculated as $`EE^{\mathrm{GGA}}[n^{\mathrm{GGA}}]+\mathrm{\Delta }[n^{\mathrm{GGA}}]`$, where $`\mathrm{\Delta }[n]=E_\mathrm{c}^{\mathrm{nl}}[n]E_\mathrm{c}^{\mathrm{grad}}[n]`$ and $`E_\mathrm{c}^{\text{grad}}[n]=E_\mathrm{c}^{\text{GGA}}[n]E_\mathrm{c}^{\text{LDA}}[n]`$. This approximation treats $`\mathrm{\Delta }`$ as a post GGA perturbation. The GGA calculations are done using the plane-wave pseudopotential corecomment  DFT code dacapo DACAPO .

The three materials considered here have layered structures with a soft direction perpendicular to the layers separation . Strong covalent bonds occur between the atoms within the hexagonal layers (lattice constant $`a`$), while weak vdW interactions occur between the layers. Graphite has a staggered or A-B type stacking with the intralayer C atoms in regular, planar hexagons stacked with corners on top of centers. Boron nitride, isoelectronic with graphite, has no shift in hexagon locations but B and N atoms in alternate positions along the $`c`$-direction. A similar alternation occurs between Mo and S atoms in the A-B type structure of MoS2 MoS2 footnote .

Calculations are also performed for bilayers of the three systems. The binding-energy curve of two parallel graphene sheets DDSSG88 , i.e. the total-energy difference at separation $`d`$ and at infinite separation, respectively, for varying $`d`$ (Fig. 2) gives in the approximation RyLuLaDi00  with vdW-DF, Eq. (5), a close relation to experimental findings for binding energy and equilibrium distance. The GGA curve, on the other hand, is completely wrong, which we blame on absence of vdW effects. The inset shows that our $`E_c^{\text{nl}}`$ contribution gives stronger binding than the traditional asymptotic vdW interaction. The binding-energy curve for two parallel BN sheets (Fig. 3) differs little from that of bulk BN as a function of lattice constant $`c`$. At equilibrium the calculated $`E_\text{c}^{\text{nl}}`$ difference is $`4`$%, attributable mostly to 2nd nearest layers in the bulk material fourpercent .

Bulk-modulus values are computed together with other structure ($`a`$,$`c`$) and bonding properties subtraction  (Table I). It is crucial to densely sample the region of ($`a`$,$`c`$) values around the optimal structure ($`a_0`$, $`c_0`$), and we use a new method ZiSc03  for direct evaluation of both structure, binding energy, and bulk modulus $`B_0`$ in the relevant range of $`a`$ and $`c`$ values B0comment . GGA values were also computed but not shown. For all three materials the various GGA flavors give no binding or bind very weakly at unreasonably large separation. The vdW-DF, on the other hand, gives values for lattice parameters and cohesive energy in good agreement and for bulk modulus in fair agreement with experimental values, when available.

In conclusion, we recommend the replacement of GGA as a standard method in total-energy calculations with vdW-DF as given in Eq. (5) for descriptions of layered systems that contain sparse electron distributions. This will give the right qualitative character of soft bonds, including saturation of the vdW potential at small separations, and even quantitative ones, like physical values of bond lengths, binding energies, and compressibilities improvements .

We are grateful to K. W. Jacobsen for suggesting tests on MoS2 layers Boll . Financial support from the Swedish Foundation for Strategic Research via Materials Consortia #9 and ATOMICS, STINT, and the Swedish Scientific Council are gratefully acknowledged. Work by M.D. and D.C.L. supported in part by NSF Grant DMR 00–93070.