atomicdata:specs:paw-xml
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| atomicdata:specs:paw-xml [2014/11/01 21:53] – Add PAWdataset example file (N.lda) Marc Torrent | atomicdata:specs:paw-xml [2015/05/18 00:25] (current) – Change def of N_c (factor 2 was missing) Marc Torrent | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| + | ====== XML specification for atomic PAW datasets ====== | ||
| + | |||
| + | < | ||
| + | //Current version of the specification: | ||
| + | //Codes implementing the PAW XML format: | ||
| + | [[https:// | ||
| + | [[http:// | ||
| + | [[http:// | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Introduction ===== | ||
| + | < | ||
| + | |||
| + | This page contains information about the PAW-XML data format for the atomic datasets | ||
| + | necessary for doing Projector Augmented-Wave calculations [(BLOCHL1994)]. | ||
| + | We use the term //dataset// instead of // | ||
| + | the PAW method is not a pseudo-potential method. | ||
| + | |||
| + | An example XML file for nitrogen PAW dataset using LDA can be seen here: {{atomicdata: | ||
| + | |||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== What defines a dataset? ===== | ||
| + | < | ||
| + | |||
| + | The following quantities define a minimum PAW dataset (the notation from Ref. [(BLOCHL2003)] is used here): | ||
| + | |||
| + | ^Quantity | ||
| + | |Z | ||
| + | |$E_\text{XC}[n]$ | ||
| + | |$E^\text{kin}_c$ | ||
| + | |$g_{\ell m}(\mathbf{r})$ | ||
| + | |$n_c(r)$ | ||
| + | |$\tilde{n}_c(r)$ | ||
| + | |$\tilde{n}_v(r)$ | ||
| + | |$\bar{v}(r)$ | ||
| + | |$\phi_i(\mathbf{r})$ | ||
| + | |$\tilde{\phi}_i(\mathbf{r})$|Pseudo partial waves | | ||
| + | |$\tilde{p}_i(\mathbf{r})$ | ||
| + | |$\Delta E^\text{kin}_{ij}$ | ||
| + | |||
| + | \\ | ||
| + | The following quantities can be optionally provided: | ||
| + | |||
| + | ^Quantity | ||
| + | |$r_{PAW}$ | ||
| + | |$v_H[\tilde{n}_{Zc}](r)$ | ||
| + | |$\tilde{Q}_{ij}(\mathbf{r})$|State-dependent shape function for compensation charge | ||
| + | |$\tau_c(r)$ | ||
| + | |$\tilde{\tau}_c(r)$ | ||
| + | |$X^{\text{core-core}}$ | ||
| + | |$X_{ij}^{\text{core-val}}$ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Specification of the elements ===== | ||
| + | < | ||
| + | |||
| + | An element looks like this: | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | or for an empty element: | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | < | ||
| + | <a href=" | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== The header ===== | ||
| + | < | ||
| + | |||
| + | The first two lines should look like this: | ||
| + | <code xml> | ||
| + | <?xml version=" | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | The first line must be present in all XML files. | ||
| + | Everything else is put inside an element with name '' | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== A comment ===== | ||
| + | < | ||
| + | |||
| + | It is recommended to put a comment giving the units and a link to this web page: | ||
| + | <code xml> | ||
| + | <!-- Nitrogen dataset for the Projector Augmented Wave method. --> | ||
| + | <!-- Units: Hartree and Bohr radii. | ||
| + | <!-- http:// | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== The '' | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | <atom symbol=" | ||
| + | </ | ||
| + | |||
| + | The '' | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Exchange-correlation ===== | ||
| + | < | ||
| + | |||
| + | The '' | ||
| + | |||
| + | The '' | ||
| + | |||
| + | The '' | ||
| + | |||
| + | < | ||
| + | Taking the names from the [[http:// | ||
| + | < | ||
| + | |||
| + | < | ||
| + | Using one of the following pre-defined aliases: | ||
| + | |||
| + | ^'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |||
| + | Examples: | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Generator ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | This element contains //character data// describing in words how the dataset was generated. | ||
| + | The '' | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Energies ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | | ||
| + | < | ||
| + | </ | ||
| + | The kinetic energy of the core electrons, $E^\text{kin}_c$, | ||
| + | The other energies are convenient to have for testing purposes and can also be useful for checking | ||
| + | the quality of the underlying atomic calculation. | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Valence states ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | <state n=" | ||
| + | <state n=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | The '' | ||
| + | defined by a unique '' | ||
| + | For each of them it is also required to provide the energy '' | ||
| + | and the matching radius of the partial waves '' | ||
| + | The number of '' | ||
| + | $\tilde{\phi}_i$ and $\tilde{p}_i$) and is noted $n_{waves}$ in the rest of this document. | ||
| + | |||
| + | For this dataset, the first two lines describe bound eigenstates with occupation numbers | ||
| + | and principal quantum numbers. Notice, that the three additional unbound states should | ||
| + | have no '' | ||
| + | In this way, we know that only the first two bound states (with '' | ||
| + | should be used for constructing an initial guess for the wave functions. | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Radial grids ===== | ||
| + | < | ||
| + | |||
| + | There can be one or more definitions of radial grids. | ||
| + | |||
| + | Example: | ||
| + | <code xml> | ||
| + | < | ||
| + | < | ||
| + | 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 | ||
| + | </ | ||
| + | < | ||
| + | 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | This defines one radial grid as $r_i = di$ where $i$ runs from 0 to 9. | ||
| + | Inside the '' | ||
| + | of the derivatives $dr_i/di$. | ||
| + | |||
| + | All functions (densities, potentials, ...) that use this grid are given as 10 numbers defining | ||
| + | the radial part of the function. The radial part of the function must be multiplied by a spherical | ||
| + | harmonics: $f_{\ell m}(\mathbf{r}) = f_\ell(r) Y_{\ell m}(\theta, \phi)$. | ||
| + | |||
| + | Each radial grid has a unique id: | ||
| + | <code xml> | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | and each numerical function must refer to one of these ids: | ||
| + | <code xml> | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | In this example, the '' | ||
| + | Each number must be separated by a '' | ||
| + | or '' | ||
| + | For numbers with scientific notation, use this format: '' | ||
| + | and not '' | ||
| + | |||
| + | A program can read the values for $r_i$ and $dr_i/di$ from the file or evaluate them from the '' | ||
| + | and associated parameter attributes. There are currently six types of radial grids: | ||
| + | |||
| + | ^'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |||
| + | The '' | ||
| + | |||
| + | Although it is possible to define as radial grids as desired, | ||
| + | it is recommended to minimize the number of grids in the dataset. | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Shape function for the compensation charge ===== | ||
| + | < | ||
| + | |||
| + | The general formulation of the compensation charge uses an expansion over the partial waves //ij// and the spherical harmonics: | ||
| + | |||
| + | $$\sum_{\ell m} C_{\ell m \ell_i m_i \ell_j m_j} \hat{Q}^{\ell}_{i j}(r) Y_{\ell m}(\theta, \phi),$$ | ||
| + | |||
| + | where $C_{\ell m \ell_i m_i \ell_j m_j}$ is a //Gaunt coefficient// | ||
| + | |||
| + | The standard expression [(BLOCHL1994)] for the //shape function// $\hat{Q}^{\ell}_{i j}(\mathbf{r})$ | ||
| + | is a product of the multipole moment $Q^{\ell}_{i j}$ and a shape function $g_l(r)$: | ||
| + | |||
| + | $$\hat{Q}^{\ell}_{i j}(r) = Q^{\ell}_{i j} g_\ell(r), | ||
| + | |||
| + | |||
| + | Several formulations [(BLOCHL1994)] [(HOLZWARTH2001)] define $g_\ell(r) \propto r^\ell k(r)$, | ||
| + | where $k(r)$ is an $l$-independent shape function: | ||
| + | |||
| + | ^'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |||
| + | Example: | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | Another formulation [(KRESSE1999)] defines directly $g_l(r)$: | ||
| + | |||
| + | ^'' | ||
| + | |'' | ||
| + | |||
| + | For '' | ||
| + | must be determined from '' | ||
| + | |||
| + | Example: | ||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | There is also a more general formulation where $\hat{Q}^{\ell}_{i j}(r)$ is given in a numerical form. | ||
| + | Several //shape functions// can be set (with the '' | ||
| + | depending on $l$ and/or combinations of partial waves (specified using the optional '' | ||
| + | and '' | ||
| + | |||
| + | Example 1, defining numerically $g_l(r)$ in $\hat{Q}^{\ell}_{i j}(r)=Q^{\ell}_{i j} g_\ell(r)$: | ||
| + | <code xml> | ||
| + | < | ||
| + | ... ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | Example 2, defining directly $\hat{Q}^{\ell}_{i j}(r)$ for states $i$='' | ||
| + | and $l$=0: | ||
| + | <code xml> | ||
| + | < | ||
| + | ... ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Radial functions ===== | ||
| + | < | ||
| + | |||
| + | Continuing, we have now reached the // | ||
| + | <code xml> | ||
| + | < | ||
| + | 6.801207147443e+02 6.801207147443e+02 6.665042896724e+02 | ||
| + | ... ... | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | The numbers inside the '' | ||
| + | '' | ||
| + | (resp. $\tilde{n}_c(\mathbf{r})$, | ||
| + | The radial part must be multiplied by $Y_{00} = (4\pi)^{-1/ | ||
| + | ($Y_{00}n_c(\mathbf{r})$ should integrate to the number of core electrons). | ||
| + | The //pseudo core density// and the //pseudo valence// density are defined similarly and | ||
| + | also have a '' | ||
| + | |||
| + | The '' | ||
| + | elements contain the radial parts of the $\phi_i(\mathbf{r})$, | ||
| + | $\tilde{\phi}_i(\mathbf{r})$ and $\tilde{p}_i(\mathbf{r})$ | ||
| + | functions for the states listed in the '' | ||
| + | (five states in the nitrogen example). | ||
| + | All functions must have an attribute '' | ||
| + | states listed in the '' | ||
| + | <code xml> | ||
| + | < | ||
| + | -8.178800366898029e+00 -8.178246914143839e+00 -8.177654917302689e+00 | ||
| + | ... ... | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | |||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | Remember that the radial part of these functions must be multiplied by a spherical harmonics: | ||
| + | $$\phi_i(\mathbf{r}) = \phi_i(r) Y_{\ell_i m_i}(\theta, | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Zero potential ===== | ||
| + | < | ||
| + | |||
| + | The zero potential, $\bar{v}$ (see section VI.D of [(BLOCHL1994)]) | ||
| + | is defined similarly to the densities; the radial part must be multiplied by | ||
| + | $Y_{00} = (4\pi)^{-1/ | ||
| + | The '' | ||
| + | radius of $\bar{v}(\mathbf{r})$: | ||
| + | <code xml> | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== The Kresse-Joubert formulation ===== | ||
| + | < | ||
| + | |||
| + | The Kresse-Joubert formulation of the PAW method [(KRESSE1999)] | ||
| + | is very similar to the original formulation of Blöchl [(BLOCHL1994)] | ||
| + | . However, the Kresse-Joubert formulation does not use $\bar{v}$ directly, | ||
| + | but indirectly through the local ionic pseudopotential, | ||
| + | Therefore, the following transformation is necessary: | ||
| + | |||
| + | $$v_H[\tilde{n}_{Zc}] = v_H[\tilde{n}_c + | ||
| + | (N_c - Z - \tilde{N}_c) g_{00} Y_{00}] + \bar{v} + | ||
| + | v_{xc}[\tilde{n}_v + \tilde{n}_c] - | ||
| + | v_{xc}[\tilde{n}_v + \tilde{n}_c + | ||
| + | (N_v - \tilde{N}_v - \tilde{N}_c) g_{00} Y_{00}]$$ | ||
| + | |||
| + | where $N_c$ is the number of core electrons, $N_v$ is the number of valence electrons, | ||
| + | $\tilde{N}_c$ is the number of electrons contained in the pseudo core density and | ||
| + | $\tilde{N}_v$ is the number of electrons contained in the pseudo valence density. | ||
| + | The Hartree potential from the density n is defined as: | ||
| + | $$v_H[n](r_1) = 4\pi \int_0^\infty r_2^2 dr_2 \frac{n(r_2)}{r_> | ||
| + | |||
| + | where $r_>$ is the larger of $r_1$ and $r_2$. | ||
| + | |||
| + | < | ||
| + | < | ||
| + | In the Kresse-Joubert formulation, | ||
| + | what we here call $\tilde{n}_v$ and in the Blöchl formulation, | ||
| + | we have $\tilde{n} = \tilde{n}_c + \tilde{n}_v$. | ||
| + | </ | ||
| + | |||
| + | It is also possible to add an element '' | ||
| + | that contains the $v_H[\tilde{n}_{Zc}](r)$ function directly, so that no conversion is necessary: | ||
| + | <code xml> | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | The '' | ||
| + | specifying the matching radius. This matching radius corresponds to the maximum of all | ||
| + | the matching radii used in the formalism. | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Kinetic energy differences ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | 1.744042161013e+00 0.000000000000e+00 2.730637956456e+00 | ||
| + | ... ... | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | This element contains the symmetric $\Delta E^\text{kin}_{ij}$ matrix: | ||
| + | |||
| + | $$\Delta E^\text{kin}_{ij} = \langle \phi_i | \hat{T} | \phi_j \rangle | ||
| + | - \langle \tilde{\phi}_i | \hat{T} | \tilde{\phi}_j \rangle$$ | ||
| + | |||
| + | where $\hat{T}$ is the kinetic energy operator used by the generator.\\ | ||
| + | With $n_{waves}$ partial waves (see [[paw-xml# | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Meta-GGA ===== | ||
| + | < | ||
| + | |||
| + | Datasets for use with MGGA functionals must also include information on the | ||
| + | //core kinetic energy density// and //pseudo core kinetic energy density// ; | ||
| + | the latters are defined with these two elements: | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | These densities are defined similarly to the core and valence densities (see above). | ||
| + | The '' | ||
| + | attribute specifying its matching radius. | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Exact exchange integrals ===== | ||
| + | < | ||
| + | |||
| + | The core-core contribution to the exact exchange energy $X^{\text{core-core}}$ | ||
| + | and the symmetric core-valence PAW-correction matrix $X_{ij}^{\text{core-valence}}$ | ||
| + | are given as: | ||
| + | |||
| + | $$X^{\text{core-core}} = -\frac{1}{4}\sum_{cc' | ||
| + | \frac{\phi_c(\mathbf{r})\phi_{c' | ||
| + | {|\mathbf{r}-\mathbf{r}' | ||
| + | |||
| + | $$X_{ij}^{\text{core-valence}} = -\frac{1}{2}\sum_c \iint d\mathbf{r} d\mathbf{r}' | ||
| + | \frac{\phi_i(\mathbf{r})\phi_c(\mathbf{r}) \phi_j(\mathbf{r}' | ||
| + | {|\mathbf{r}-\mathbf{r}' | ||
| + | |||
| + | The $X_{ij}^{\text{core-valence}}$ coefficients depend only on pairs of the radial | ||
| + | basis functions $\phi_i(r)$ and can be evaluated by summing over radial | ||
| + | integrals times **3-j** symbols according to: | ||
| + | |||
| + | $$X_{ij}^{\text{core-valence}} = | ||
| + | -\delta_{l_i l_j} \delta_{m_i m_j} \sum_{c L} \frac{N_c}{2} | ||
| + | {\begin{pmatrix}l_c & L & l_i \\ 0 & 0 & 0\end{pmatrix}}^2 | ||
| + | \int r^2 dr \int {r'}^2 d{r'} | ||
| + | \frac{r^{L}_{< | ||
| + | \phi_i(r) \phi_c(r) \phi_j(r' | ||
| + | |||
| + | where\\ | ||
| + | $N_{c}$ is the number of core electrons corresponding to $l_{c}$, namely $N_{c}=2(2l_{c}+1)$, | ||
| + | $r_>$ (resp. $r_<$) is the larger (resp. smaller) of $r$ and $r'$. | ||
| + | |||
| + | $X^{\text{core-core}}$ can be specified in the '' | ||
| + | element.\\ | ||
| + | With $n_{waves}$ partial waves (see [[paw-xml# | ||
| + | $X_{ij}^{\text{core-valence}}$ is a $n_{waves} \times n_{waves}$ matrix. | ||
| + | It can be specified as $n_{waves}^2$ numbers inside the '' | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | ... ... | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Optional elements ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | < | ||
| + | </ | ||
| + | |||
| + | Although not necessary, it may be helpful to provide the following item(s) in the dataset: | ||
| + | |||
| + | * Radius of the PAW augmentation region '' | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== End of the dataset ===== | ||
| + | < | ||
| + | |||
| + | <code xml> | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== How to use the datasets ===== | ||
| + | < | ||
| + | |||
| + | Most likely, the radial functions will be needed on some other type of radial grid than | ||
| + | the one used in the dataset. The idea is that one should read in the radial functions | ||
| + | and then transform them to the radial grids used by the specific implementation. | ||
| + | After the transformation, | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== Plotting the radial functions ===== | ||
| + | < | ||
| + | |||
| + | The first 10-20 lines of the XML-datasets, | ||
| + | and should give an overview of what kind of dataset it is and how it was generated. | ||
| + | The remaining part of the file contains numerical data for all the radial functions. | ||
| + | To get an overview of these functions, you can extract that data with the | ||
| + | '' | ||
| + | |||
| + | < | ||
| + | < | ||
| + | is very primitive and is only included in order to demonstrates how to parse XML using | ||
| + | SAX from a Python program. Parsing XML from Fortran or C code with SAX should be similar. | ||
| + | </ | ||
| + | |||
| + | <file python pawxml.py> | ||
| + | # | ||
| + | from __future__ import print_function | ||
| + | import os | ||
| + | import sys | ||
| + | import xml.sax | ||
| + | from optparse import OptionParser | ||
| + | from math import exp, log | ||
| + | |||
| + | class Reader(xml.sax.handler.ContentHandler): | ||
| + | def __init__(self, | ||
| + | self.list = list | ||
| + | self.name = name | ||
| + | self.state = state | ||
| + | self.grid = {} | ||
| + | xml.sax.handler.ContentHandler.__init__(self) | ||
| + | def read(self, filename): | ||
| + | if filename.endswith(' | ||
| + | import gzip | ||
| + | source = gzip.open(filename) | ||
| + | else: | ||
| + | source = open(filename) | ||
| + | xml.sax.parse(source, | ||
| + | def startElement(self, | ||
| + | if name == ' | ||
| + | print(attrs[' | ||
| + | elif name == ' | ||
| + | istart = int(attrs[' | ||
| + | iend = int(attrs[' | ||
| + | ii = range(istart, | ||
| + | id = attrs[' | ||
| + | eq = attrs[' | ||
| + | if eq == ' | ||
| + | a = float(attrs[' | ||
| + | d = float(attrs[' | ||
| + | self.grid[id] = [a * exp(d * i) for i in ii] | ||
| + | elif eq == ' | ||
| + | a = float(attrs[' | ||
| + | n = float(attrs[' | ||
| + | self.grid[id] = [a * i / (n - i) for i in ii] | ||
| + | elif eq == ' | ||
| + | a = float(attrs[' | ||
| + | d = float(attrs[' | ||
| + | self.grid[id] = [a * (exp(d * i) - 1.0) for i in ii] | ||
| + | elif eq == ' | ||
| + | d = float(attrs[' | ||
| + | self.grid[id] = [d * i for i in ii] | ||
| + | elif eq == ' | ||
| + | a = float(attrs[' | ||
| + | n = float(attrs[' | ||
| + | self.grid[id] = [(i / n + a)**5 / a - a**4 for i in ii] | ||
| + | else: | ||
| + | raise RuntimeError(' | ||
| + | elif name == self.name and attrs.get(' | ||
| + | self.r = self.grid[attrs[' | ||
| + | self.data = '' | ||
| + | else: | ||
| + | self.data = None | ||
| + | def characters(self, | ||
| + | if self.data is not None: | ||
| + | self.data += data | ||
| + | def endElement(self, | ||
| + | if self.data is not None: | ||
| + | for r, x in zip(self.r, self.data.split()): | ||
| + | print(r, x) | ||
| + | | ||
| + | op = OptionParser(usage=' | ||
| + | version=' | ||
| + | op.add_option(' | ||
| + | help=' | ||
| + | metavar='< | ||
| + | op.add_option(' | ||
| + | help=' | ||
| + | metavar='< | ||
| + | op.add_option(' | ||
| + | help=' | ||
| + | options, args = op.parse_args() | ||
| + | if len(args) != 1: | ||
| + | op.error(' | ||
| + | |||
| + | reader = Reader(options.list, | ||
| + | reader.read(args[0]) | ||
| + | </ | ||
| + | |||
| + | Usage: | ||
| + | |||
| + | It works like this: | ||
| + | < | ||
| + | $ pawxml.py [options] dataset[.gz] | ||
| + | </ | ||
| + | |||
| + | Options: | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |'' | ||
| + | |||
| + | Examples: | ||
| + | < | ||
| + | [~]$ pawxml.py -x pseudo_core_density N.LDA | xmgrace - | ||
| + | [~]$ pawxml.py -x ae_partial_wave -s N2p N.LDA > N.ae.2p | ||
| + | [~]$ pawxml.py -x pseudo_partial_wave -s N2p N.LDA > N.ps.2p | ||
| + | [~]$ xmgrace N.??.2p | ||
| + | </ | ||
| + | |||
| + | \\ \\ | ||
| + | < | ||
| + | ===== References ===== | ||
| + | < | ||
| + | |||
| + | [(BLOCHL1994> | ||
| + | [(BLOCHL2003> | ||
| + | [(KRESSE1999> | ||
| + | [(HOLZWARTH2001> | ||
| + | [(LAASONEN1993> | ||
| + | |||
| + | < | ||
| + | refnote-id | ||
| + | reference-format | ||
| + | reference-base | ||
| + | multi-ref-id | ||
| + | note-id-format | ||
| + | note-id-base | ||
| + | back-ref-base | ||
| + | back-ref-format | ||
| + | back-ref-caret | ||
| + | notes-separator | ||
| + | </ | ||
| + | ~~REFNOTES~~ | ||
| + | |||