From 0391d166d6d28007119171d2c09f39ce899c06de Mon Sep 17 00:00:00 2001 From: giannozz Date: Thu, 11 May 2006 08:07:42 +0000 Subject: [PATCH] Documentation updated git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3115 c92efa57-630b-4861-b058-cf58834340f0 --- Doc/BUGS | 8 ++++ Doc/CREDITS | 91 +++++++++++++++++++++++++++------------------ Doc/INPUT_PP | 4 +- Doc/INPUT_PW | 11 ++++-- Doc/refman.tex | 13 +++++++ Doc/restart | 12 +++--- Doc/users-guide.tex | 85 ++++++++++++++++++++++-------------------- 7 files changed, 136 insertions(+), 88 deletions(-) diff --git a/Doc/BUGS b/Doc/BUGS index 9a22fd20f..acdd59a86 100644 --- a/Doc/BUGS +++ b/Doc/BUGS @@ -1,3 +1,11 @@ +Fixed in version 3.1: + + * various problems in stress calculation, both in PW and in CP + + * in phonon dispersion calculation, the threshold for diagonalization + was not always what was expected to be. Minor numerical differences + could result. + Fixed in version 3.0: * latgen.f90 : case ibrav=13 bad diff --git a/Doc/CREDITS b/Doc/CREDITS index 1c9fc1812..a27965064 100644 --- a/Doc/CREDITS +++ b/Doc/CREDITS @@ -9,46 +9,66 @@ and of several utilities, in particular: - the "atomic" pseudopotential generation code. - the Input/Output Toolkit "iotk" -The maintenance and further development of the Quantum-ESPRESSO code is -promoted by the DEMOCRITOS National Simulation Center of the Italian -INFM (http://www.democritos.it/), under the coordination of Paolo -Giannozzi (p.giannozzi@sns.it) (Scuola Normale Superiore, Pisa), with -the strong support of the CINECA National Supercomputing Center in -Bologna (http://www.cineca.it/), under the responsibility of Carlo -Cavazzoni (c.cavazzoni@cineca.it). +The maintenance and further development of the Quantum-ESPRESSO code +is promoted by the DEMOCRITOS National Simulation Center of the +Italian INFM (http://www.democritos.it/), under the coordination of +Paolo Giannozzi (Scuola Normale Superiore, Pisa), with the strong +support of the CINECA National Supercomputing Center in Bologna +(http://www.cineca.it/), under the responsibility of Carlo +Cavazzoni (CINECA, Bologna). -Currently active developers include Gerardo Ballabio (CINECA), -Stefano Fabris, Guido Fratesi, Adriano Mosca Conte (SISSA, Trieste), -Anton Kokalj (Joszef Stefan Institute, Ljubljana), Carlo Sbraccia -(Princeton). +The PWscf package (http://www.pwscf.org) was developed by Stefano Baroni, +Stefano de Gironcoli, Andrea Dal Corso (SISSA, Trieste), Paolo Giannozzi, +and many others. +Matteo Cococcioni (MIT) and SdG implemented LDA+U. +Michele Lazzeri (Paris VI) implemented the 2n+1 code and Raman cross +section calculation with 2nd-order response. +Oswaldo Dieguez (Rutgers) implemented Berry's phase calculations. +Ralph Gebauer (ICTP, Trieste) and Adriano Mosca Conte (SISSA, Trieste) +implemented noncolinear magnetism, AdC the spin-orbit. +Mickael Profeta (Paris VI) implemented electric-field gradients. +Carlo Sbraccia (Princeton) implemented NEB. +Alexander Smogunov (SISSA) and AdC implemented ballistic conductance. +Paolo Umari (MIT) implemented finite electric fields. +Xiaofei Wang (Princeton) and Carlo Sbraccia implemented META-GGA. +Renata Wentzcovitch (UMinn) implemented variable-cell molecular dynamics. +Yudong Wu (Princeton) and Carlo Sbraccia implemented Metadynamics. -The PWscf package was developed by Stefano Baroni, Stefano -de Gironcoli, Andrea Dal Corso (SISSA), Paolo Giannozzi, and others. -The web site for PWSCF and related codes is: http://www.pwscf.org/ +The CP code is based on the original code written by Roberto Car and +Michele Parrinello. CP was developed by Alfredo Pasquarello (IRRMA, +Lausanne), Kari Laasonen (Oulu), Andrea Trave (LLNL), Roberto Car +(Princeton), Nicola Marzari (MIT), Paolo Giannozzi, and others. +Also developed by former FPMD team: Carlo Cavazzoni, +Gerardo Ballabio (CINECA), Sandro Scandolo (ICTP), +Guido Chiarotti (SISSA), Paolo Focher, and others. +Yosuke Kanai (Princeton) implemented Fourier strings method. +Manu Sharma (Princeton) implemented dynamics with Wannier functions. +Paolo Umari (MIT) implemented finite electric fields and conjugate gradients. +Paolo Umari and Ismaila Dabo (MIT) implemented ensemble-DFT. +Xiaofei Wang (Princeton) and Carlo Sbraccia (Princeton) implemented META-GGA. +Yudong Wu (Princeton) and Carlo Sbraccia implemented Metadynamics. +Yudong Wu and Manu Sharma implemented maximally localized Wannier +functions. +The Autopilot feature was implemented by Targacept, Inc. -The CP code is based on the original code written by -Roberto Car and Michele Parrinello. +Gerardo Ballabio implemented "configure" for Quantum-Espresso. -CP was developed by Alfredo Pasquarello (IRRMA, Lausanne), Kari -Laasonen (Oulu), Andrea Trave (LLNL), Roberto Car (Princeton), -Nicola Marzari (MIT), Paolo Giannozzi, and others. -Also developed by former FPMD team: Carlo Cavazzoni, Gerardo Ballabio (CINECA), -Sandro Scandolo (ICTP, Trieste), Guido Chiarotti (SISSA), Paolo -Focher, and others. - -PWgui was written by Anton Kokalj (IJS) and is based on his GUIB -concept (http://www-k3.ijs.si/kokalj/guib/). +PWgui was written by Anton Kokalj (IJS, Ljubljana) and is based on his +GUIB concept (http://www-k3.ijs.si/kokalj/guib/). The pseudopotential generation package "atomic" was written by Andrea Dal Corso and it is the result of many additions to -the original code by Paolo Giannozzi. +the original code by Paolo Giannozzi and others. The input/output toolkit "iotk" (http://www.s3.infm.it/iotk) -was written by Giovanni Bussi (S3 Modena). +was written by Giovanni Bussi (S3, Modena). + +The frozen-phonon code was contributed by Silviu Zilberman +(Princeton). The calculation of the finite (imaginary) frequency molecular polarizability using the approximated Thomas-Fermi + von Weizaecker -scheme was contributed by Huy-Viet Nguyen (Sissa), +scheme was contributed by Huy-Viet Nguyen (SISSA), The BlueGene porting was done by Costas Bekas and Alessandro Curioni (IBM Zurich). @@ -56,14 +76,13 @@ The BlueGene porting was done by Costas Bekas and Alessandro Curioni A list of further contributors includes: Dario Alfe', Francesco Antoniella, Mauro Boero, Nicola Bonini, Claudia Bungaro, Paolo Cazzato, Davide Ceresoli, Gabriele Cipriani, -Matteo Cococcioni, Cesar Da Silva, Alberto Debernardi, Gernot Deinzer, -Oswaldo Dieguez, Andrea Ferretti, Ralph Gebauer, Martin Hilgeman, -Eyvaz Isaev, Yosuke Kanai, Axel Kohlmeyer, Konstantin Kudin, -Michele Lazzeri, Sergey Lisenkov, Kurt Maeder, Francesco Mauri, -Nicolas Mounet, Pasquale Pavone, Mickael Profeta, Guido Roma, -Manu Sharma, Alexander Smogunov, Kurt Stokbro, Pascal Thibaudeau, -Antonio Tilocca, Paolo Umari, Renata Wentzcovitch, Malgorzata Wierzbowska, -Xiaofei Wang, Yudong Wu, and let us apologize to everybody we have forgotten. +Cesar Da Silva, Alberto Debernardi, Gernot Deinzer, Andrea Ferretti, +Guido Fratesi, Martin Hilgeman, Eyvaz Isaev, Axel Kohlmeyer, +Konstantin Kudin, Sergey Lisenkov, Kurt Maeder, Francesco Mauri, +Riccardo Mazzarello, Nicolas Mounet, Pasquale Pavone, Guido Roma, +Kurt Stokbro, Paul Tangney, Pascal Thibaudeau, Antonio Tilocca, +Jaro Tobik, Malgorzata Wierzbowska, +and let us apologize to everybody we have forgotten. All the material included in this distribution is free software; you can redistribute it and/or modify it under the terms of the GNU diff --git a/Doc/INPUT_PP b/Doc/INPUT_PP index 603cf8a90..a5d9e3124 100644 --- a/Doc/INPUT_PP +++ b/Doc/INPUT_PP @@ -52,7 +52,7 @@ ! if emax is not specified, emax=E_fermi ! 11=the V_bare + V_H potential ! 12=the electric field potential - ! 13=the noncolinear magnetization. + ! 13=the noncollinear magnetization. ! ! ! plot_num=7 in the noncollinear case, plot the contribution of the @@ -94,7 +94,7 @@ ! emax upper energy boundary (in eV), i.e. compute ! ILDOS from emin to emax ! - ! Options for noncolinear magnetization + ! Options for noncollinear magnetization ! ! spin_component 0=absolute value (default value) ! 1=x component of the magnetization diff --git a/Doc/INPUT_PW b/Doc/INPUT_PW index 86bf97f69..5231a2220 100644 --- a/Doc/INPUT_PW +++ b/Doc/INPUT_PW @@ -299,7 +299,7 @@ nspin INTEGER nspin = 1 : non-polarized calculation (default) nspin = 2 : spin-polarized calculation, LSDA (magnetization along z axis) - nspin = 4 : spin-polarized calculation, noncolinear + nspin = 4 : spin-polarized calculation, noncollinear (magnetization in generic direction) DO NOT specify nspin in this case; specify "noncolin=.TRUE." instead @@ -329,18 +329,21 @@ nelup, neldw REAL Note that this fixes the final value of the magnetization. The sum must yield nelec that must also be specified explicitly in this case. Not valid for spin-unpolarized - or noncolinear calculations, only for LSDA. Obsolescent. + or noncollinear calculations, only for LSDA. Obsolescent: + use multiplicity or tot_magnetization instead. multiplicity INTEGER ( default = 0 [unspecified] ) spin multiplicity (2s+1). 1 is singlet, 2 for doublet etc. Note that this fixes the final value of the magnetization. if unspecified or a non-zero value is specified in nelup/neldw then multiplicity variable is ignored. + Do not specify both multiplicity and tot_magnetization. tot_magnetization INTEGER ( default = -1 [unspecified] ) majority spin - minority spin (nelup - neldw). if unspecified or a non-zero value is specified in nelup/neldw then tot_magnetization variable is ignored. + Do not specify both multiplicity and tot_magnetization. YES, there is redundancy! nelup/neldw are enough to specify the spin state. However these variables are not very convenient and will be eliminated from the input in future versions. @@ -420,13 +423,13 @@ eamp REAL ( default = 0.001 a.u. ) angle1(i) REAL The angle expressed in degrees between the initial - magnetization and the z-axis. For noncolinear calculations + magnetization and the z-axis. For noncollinear calculations only. I runs over the atom types. angle2(i) REAL The angle expressed in degrees between the projection of the initial magnetization on x-y plane and the x-axis. - For noncolinear calculations only. + For noncollinear calculations only. constrained_magnetization CHARACTER ( defalt = 'none' ) Used to perform constrained calculations in magnetic systems diff --git a/Doc/refman.tex b/Doc/refman.tex index 637d5b608..0f0aca8aa 100644 --- a/Doc/refman.tex +++ b/Doc/refman.tex @@ -291,6 +291,19 @@ that take little memory are replicated, those that take a lot of memory (wavefunctions, G-vectors, R-space grid) are distributed. +Beware: replicated calculations may either be performed independently +on each processor, or performed on one processor and broadcast to all +others. The first approach requires less programming, but it is unsafe: +in principle all processors should yield exactly the same results, if +they work on the same data, but sometimes they don't (depending on the +machine, compiler, and libraries). Even a tiny difference in the last +significant digit can eventually cause serious trouble if allowed to +build up, especially when a replicated check is performed (in which +case the code may "hang" if the check yields different results on +different processors). Never assume that the value of a variable +produced by replicated calculations is exactly the same on all processors: +when in doubt, broadcast the value calculated on a specific processor. + \subsection{Paradigms} \subsection{Implementation} \subsubsection{Data distribution} diff --git a/Doc/restart b/Doc/restart index d40f25142..d68a238e0 100644 --- a/Doc/restart +++ b/Doc/restart @@ -1,6 +1,6 @@ Quantum-Espresso restart file specifications - VERY PRELIMINARY -Paolo Giannozzi scripsit AD 2005-11-11 +Paolo Giannozzi scripsit AD 2005-11-11 - Last modified 2006-05-10 0) rationale @@ -31,12 +31,12 @@ Solutions: atomic structure, lattice, symmetries, parameters of the run, ... - pointers to other files or directories containing bulkier data, such as wavefunctions, charge density, potentials: - - File "charge_density.rho" + - File "charge_density.xml" contains the charge density - - File "charge_density.rhoup" - contains the spin-up charge density (LSDA calculations) - - File "charge_density.rhodw" - contains the spin-down charge density (LSDA calculations) + - File "spin_polarization.xml" + contains the spin polarization (rhoup-rhodw) (LSDA calculations) + - Files "magnetization.x", "magnetization.y", "magnetization.z": + contain the spin polarization (noncollinear calculations) - File "mat_z.1" contains occupations (ensemble-dynamics only) - File "lambda.dat" diff --git a/Doc/users-guide.tex b/Doc/users-guide.tex index b4fb7a6e3..15a2540f1 100644 --- a/Doc/users-guide.tex +++ b/Doc/users-guide.tex @@ -109,7 +109,7 @@ All of the above work for both insulators and metals, in any crystal structure, for many exchange-correlation functionals (including spin polarization and LDA+U), for both norm-conserving (Hamann-Schl\"uter-Chiang) pseudopotentials in separable form, and --- with very few exceptions ---- for Ultrasoft (Vanderbilt) pseudopotentials. Non-colinear +--- for Ultrasoft (Vanderbilt) pseudopotentials. Non-collinear magnetism and spin-orbit interactions are also implemented. Finite electric fields are implemented in both the supercell and the ``modern theory of polarization'' approaches (the latter is still @@ -141,46 +141,56 @@ Both are at an experimental stage. \hyphenation{gian-noz-zi} The maintenance and further development of the Quantum-ESPRESSO code is promoted by the DEMOCRITOS National Simulation Center of INFM (Italian -institute for condensed matter physics) under the coordination of +Institute for Condensed Matter Physics) under the coordination of Paolo Giannozzi (Scuola Normale Superiore, Pisa), with the strong support of the CINECA National Supercomputing Center in Bologna under the responsibility of Carlo Cavazzoni. -Currently active developers include -Gerardo Ballabio (CINECA), -Stefano Fabris, -Adriano Mosca Conte, -Carlo Sbraccia (SISSA, Trieste), -Anton Kokalj (Jo\v{z}ef Stefan Institute, Ljubljana). The PWscf package was originally developed by Stefano Baroni, Stefano -de Gironcoli, Andrea Dal Corso (SISSA), Paolo Giannozzi, and others. +de Gironcoli, Andrea Dal Corso (SISSA), Paolo Giannozzi, and many +others, in particular:\\ +-- Matteo Cococcioni (MIT) and SdG implemented LDA+U. \\ +-- Michele Lazzeri (Paris VI) implemented the $2n+1$ code and Raman cross +section calculation with 2nd-order response.\\ +-- Oswaldo Dieguez (Rutgers) implemented Berry's phase calculations.\\ +-- Ralph Gebauer (ICTP, Trieste) and Adriano Mosca Conte (SISSA, Trieste) +implemented noncolinear magnetism, AdC the spin-orbit.\\ +-- Mickael Profeta (Paris VI) implemented electric-field gradients.\\ +-- Carlo Sbraccia (Princeton) implemented NEB. \\ +-- Alexander Smogunov (SISSA) and AdC implemented ballistic conductance.\\ +-- Paolo Umari (MIT) implemented finite electric fields.\\ +-- Xiaofei Wang (Princeton) and Carlo Sbraccia implemented META-GGA.\\ +-- Renata Wentzcovitch (UMinn) implemented variable-cell molecular dynamics.\\ +-- Yudong Wu (Princeton) and Carlo Sbraccia implemented Metadynamics. -The CP code is the result of the merging of two codes: CP and FPMD, -both based on the original code written by Roberto Car and Michele -Parrinello. -CP was developed by -Alfredo Pasquarello (IRRMA, Lausanne), -Kari Laasonen (Oulu), -Andrea Trave (LLNL), -Roberto Car (Princeton), -Nicola Marzari (MIT), -Paolo Giannozzi, -and others. -FPMD was developed by -Carlo Cavazzoni, -Gerardo Ballabio (CINECA), -Sandro Scandolo (ICTP, Trieste), -Guido Chiarotti (SISSA), -Paolo Focher, -and others. +The CP code is based on the original code written by Roberto Car and +Michele Parrinello. CP was developed by Alfredo Pasquarello (IRRMA, +Lausanne), Kari Laasonen (Oulu), Andrea Trave (LLNL), Roberto Car +(Princeton), Nicola Marzari (MIT), Paolo Giannozzi, and by former +FPMD team: Carlo Cavazzoni, Gerardo Ballabio (CINECA), Sandro Scandolo +(ICTP), Guido Chiarotti (SISSA), Paolo Focher, and others. +In particular:\\ +-- Yosuke Kanai (Princeton) implemented Fourier strings method.\\ +-- Manu Sharma (Princeton) implemented dynamics with Wannier functions.\\ +-- Paolo Umari (MIT) implemented finite electric fields and conjugate +gradients.\\ +-- Paolo Umari and Ismaila Dabo (MIT) implemented ensemble-DFT.\\ +-- Xiaofei Wang (Princeton) and Carlo Sbraccia (Princeton) implemented META-GGA.\\ +-- Yudong Wu (Princeton) and Carlo Sbraccia implemented Metadynamics.\\ +-- Yudong Wu and Manu Sharma implemented maximally localized Wannier +functions.\\ +-- The Autopilot feature was implemented by Targacept, Inc. -PWgui was written by Anton Kokalj and is based on his GUIB concept +Gerardo Ballabio implemented "configure" for Quantum-Espresso. + +PWgui was written by Anton Kokalj (Jo\v{z}ef Stefan Institute, Ljubljana) +and is based on his GUIB concept (\htmladdnormallink{\texttt{http://www-k3.ijs.si/kokalj/guib/}}% {http://www-k3.ijs.si/kokalj/guib/}). The pseudopotential generation package ``atomic'' was written by Andrea Dal Corso and it is the result of many additions to the -original code by Paolo Giannozzi. +original code by Paolo Giannozzi and others. \hyphenation{mo-de-na} The input/output toolkit ``iotk'' @@ -188,6 +198,9 @@ The input/output toolkit ``iotk'' {http://www.s3.infm.it/iotk/}) was written by Giovanni Bussi (S3, Modena). +The calculation of the finite (imaginary) frequency molecular +polarizability using the approximated Thomas-Fermi + von Weizaecker +scheme was contributed by Huy-Viet Nguyen (SISSA), The frozen-phonon code was contributed by Silviu Zilberman (Princeton). @@ -213,33 +226,25 @@ Matteo Cococcioni, Cesar Da Silva, Alberto Debernardi, Gernot Deinzer, -Oswaldo Dieguez, Andrea Ferretti, Guido Fratesi, -Ralph Gebauer, Martin Hilgeman, Eyvaz Isaev, -Yosuke Kanai, Axel Kohlmeyer, Konstantin Kudin, -Michele Lazzeri, Sergey Lisenkov, Kurt Maeder, Francesco Mauri, +Riccardo Mazzarello, Nicolas Mounet, Pasquale Pavone, -Mickael Profeta, Guido Roma, -Manu Sharma, -Alexander Smogunov, Kurt Stokbro, +Paul Tangney, Pascal Thibaudeau, Antonio Tilocca, -Paolo Umari, -Renata Wentzcovitch, +Jaro Tobik, Malgorzata Wierzbowska, -Xiaofei Wang, -Yudong Wu, and let us apologize to everybody we have forgotten. This guide was mostly written by Paolo Giannozzi, Gerardo Ballabio,