BerkeleyGW manual (trunk revision 7293)

Contents

  1. SECTION:Preliminaries
  2. README
  3. license.txt
  4. CONTRIBUTORS
  5. documentation/LITERATURE.html
  6. config/README
  7. testsuite/README
  8. library/README
  9. examples/README
  10. END
  11. SECTION:MeanField
  12. MeanField/README
  13. SECTION:ESPRESSO
  14. MeanField/ESPRESSO/README
  15. MeanField/ESPRESSO/kgrid.inp
  16. MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.html
  17. MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.html
  18. MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.html
  19. MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.html
  20. MeanField/ESPRESSO/version-4.3.2/pw2bgw.inp
  21. MeanField/ESPRESSO/version-4.3.2/bgw2pw.inp
  22. MeanField/ESPRESSO/version-4.3.2/README_patch
  23. MeanField/ESPRESSO/patch_oldversions/README
  24. END
  25. SECTION:PARATEC
  26. MeanField/PARATEC/README
  27. END
  28. SECTION:SIESTA
  29. MeanField/SIESTA/README
  30. MeanField/SIESTA/patch/README
  31. MeanField/SIESTA/siesta2bgw.inp
  32. END
  33. SECTION:Octopus
  34. MeanField/Octopus/README
  35. END
  36. SECTION:EPM
  37. MeanField/EPM/README
  38. MeanField/EPM/epm.inp
  39. END
  40. SECTION:ICM
  41. MeanField/ICM/README
  42. END
  43. SECTION:Utilities
  44. MeanField/Utilities/README
  45. MeanField/Utilities/wfnmerge.inp
  46. MeanField/Utilities/fix_occ.inp
  47. END
  48. SECTION:SAPO
  49. MeanField/SAPO/README
  50. MeanField/SAPO/sapo.inp
  51. END
  52. END
  53. SECTION:Epsilon
  54. Epsilon/README
  55. Epsilon/epsilon.inp
  56. Epsilon/epsconv.inp
  57. Epsilon/epsomega.inp
  58. Epsilon/epsinvomega.inp
  59. Epsilon/epsmat_merge.inp
  60. Epsilon/epsmat_old2hdf5.inp
  61. END
  62. SECTION:Sigma
  63. Sigma/README
  64. Sigma/sigma.inp
  65. Sigma/sig2wan.inp
  66. END
  67. SECTION:BSE
  68. BSE/README_kernel
  69. BSE/kernel.inp
  70. BSE/README_absorption
  71. BSE/absorption.inp
  72. BSE/inteqp.inp
  73. BSE/README_inteqp
  74. BSE/summarize_eigenvectors.inp
  75. END
  76. SECTION:PlotXct
  77. PlotXct/README
  78. PlotXct/plotxct.inp
  79. END
  80. SECTION:Visual
  81. Visual/README
  82. Visual/surface.inp
  83. Visual/gsphere.inp
  84. END
  85. SECTION:Developers
  86. doxygen/README
  87. Common/README
  88. Common/qhull/README
  89. MeanField/spglib-1.0.9/README
  90. END

About

This manual is assembled automatically from the various documentation files in the BerkeleyGW distribution. The headings are the paths and filenames. For each executable, consult the corresponding .inp file for information about input parameters. The homepage is http://www.berkeleygw.org.

Preliminaries

README

BerkeleyGW is a GW / Bethe-Salpeter equation computer package. Documentation ------------- The user documentation is gathered in the directory ~BerkeleyGW/documentation/users/ Compilation ----------- We have tested the code extensively with various configurations, and support the following compilers and libraries: * Operating systems: Linux, AIX, MacOS * Fortran compilers (required): pgf90, ifort, gfortran, g95, openf90, sunf90, pathf90, crayftn, af90 (Absoft), nagfor, xlf90 (experimental) * C compilers (required): pgcc, icc, gcc, opencc, pathcc, craycc, clang * C++ compilers (required): pgCC, icpc, g++, openCC, pathCC, crayCC, clang++ * MPI implementation (optional): OpenMPI, MPICH1, MPICH2, MVAPICH2, Intel MPI * LAPACK/BLAS implementation (required): NetLib, ATLAS, Intel MKL, ACML, Cray LibSci * ScaLAPACK/BLACS implementation (required if MPI is used): NetLib, Cray LibSci, Intel MKL, AMD * FFTW (required): versions 3.3.x 1. Architecture-specific Makefile-include files appropriate for various supercomputers as well as for using standard Ubuntu or Macports packages are provided in the config directory. Copy or link one to the top directory. Example: cp config/stampede.tacc.utexas.edu_threaded_hdf5.mk arch.mk 2. Edit it to fit your needs. Refer to config/README for details. 3. Copy flavor_real.mk or flavor_cplx.mk to flavor.mk to set flavor. Complex may always be used. Real may be used for systems that have both inversion (about the origin) and time-reversal symmetry, and will be faster and use less memory. 4. Stay in the root directory and run the following commands to compile the various codes: MAIN: make epsilon make sigma make bse MISC: make plotxct make nonlinearoptics make meanfield make visual EVERYTHING: make all All codes/packages (for selected flavor) make -j all parallel build (for selected flavor) make all-flavors everything, for both flavors make -j all-flavors parallel build of everything, for both flavors make install INSTDIR= install binaries, library, examples, testsuite into specified prefix These commands will generate executables with extension .x in the source directory and symbolic links with the same name in the bin directory. 5. Test your build. See testsuite/README for more info. License ------- BerkeleyGW is distributed under the Berkeley Software Distribution (BSD) license. For license information see "license.txt" as well as "Copyright.txt" Contributors ------------ See the file CONTRIBUTORS for a complete list of authors.

license.txt

Unless otherwise stated, all files distributed in this package are licensed under the following terms. BerkeleyGW, Copyright (c) 2011, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. (2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.

CONTRIBUTORS

Chronological list of contributors ---------------------------------- BerkeleyGW - The Berkeley GW (And More) Package http://www.berkeleygw.org Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) - Version 1.0 (Aug, 2011) J. Deslippe, G. Samsonidze, D. A. Strubbe, M. Jain Version 0.5 (July, 2008) J. Deslippe, G. Samsonidze, L. Yang, F. Ribeiro Version 0.2 M. L. Tiago (2001) Original BSE Code, PlotXct S. Ismail-Beigi (2002) FFT, Documentation, General Improvements C. Spataru (2005) Cylindrical Coulomb Truncation, Transform (obsolete) Version 0.1 X. Blase (1998) Implemented F90, Preprocessing, Dynamical Memory Allocation G. M. Rignanese " " E. Chang " " Version 0.0 M. Hybertsen (1985) Original GW Code Report current bugs or problems and ask questions at the BerkeleyGW Forum, at http://www.berkeleygw.org. Alphabetical list of contributors --------------------------------- Gabriel K. Antonius (GKA) Brad A. Barker (BAB) Xavier Blase (XAV) Andrew Canning (AC) Andrea Cepellotti (ACE) Eric K. Chang (EKC) Sangkook Choi (SKC) Mauro Del Ben (MDB) Jack R. Deslippe (JRD) Peter W. Doak (PWD) Mark S. Hybertsen (MSH) Sohrab Ismail-Beigi (SIB) Manish Jain (MJ) Felipe H. da Jornada (FHJ) Je-Luen Li (JLL) Zhenglu Li (ZL) Steven G. Louie (SGL) Andrei S. Malashevich (ASM) Brad D. Malone (BDM) Jamal I. Mustafa (JIM) Jeffrey B. Neaton (JBN) Cheol-Hwan Park (CHP) David G. Prendergast (DGP) Diana Y. Qiu (DYQ) Tonatiuh Rangel (TR) Filipe J. Ribeiro (FJR) Gian-Marco Rignanese (GMR) Georgy Samsonidze (GSM) Sahar Sharifzadeh (SS) Catalin D. Spataru (CDS) David A. Strubbe (DAS) Murilo L. Tiago (MLT) Derek Vigil-Fowler (DVF) Li Yang (LY) Oleg V. Yazyev (OVY) Peihong Zhang (PZ)

documentation/LITERATURE.html

Please let us know when your paper is published with BerkeleyGW for inclusion here (or any other additions or corrections) in the Forum, under the "Literature" topic.

I. Papers on the implementation of BerkeleyGW
  1. Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, "BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures," Comput. Phys. Commun. 183, 1269 (2012) (most up-to-date on arXiV)
  2. Mark S. Hybertsen and Steven G. Louie, "Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies," Phys. Rev. B 34, 5390 (1986) [GW, GPP, COHSEX] Errata: Eq. 11 should have E' instead of E in the numerator. Eq. 32 should have Ω2 rather than Ω in the numerator. Eq. 34a should have δG,G instead of 1 in the parentheses.
  3. Sheng Bai Zhang, David Tománek, Marvin L. Cohen, Steven G. Louie, and Mark S. Hybertsen, "Evaluation of quasiparticle energies for semiconductors without inversion symmetry," Phys. Rev. B 40, 3162 (1989) [GPP for systems without inversion symmetry] Note: ε1 and ε2 in this paper refer to the Hermitian and Antihermitian components of the dielectric matrix, respectively, and not to the real and imaginary parts of ε. See D. J. Johnson, Phys. Rev. B 9, 4475 (1974).
  4. Michael Rohlfing and Steven G. Louie, "Electron-hole excitations and optical spectra from first principles," Phys. Rev. B 62, 4927 (2000) [BSE] Errata: Eqs. 26 and 27 should have 8π2 instead of 16π in the prefactor. Eq. 44 should be a sum over G ≠ 0. Eq. 45 should have ε-1G,G' instead of ε-1G,0.
  5. Je-Luen Li, Gian-Marco Rignanese, Eric K. Chang, Xavier Blase, and Steven G. Louie, "GW study of the metal-insulator transition of bcc hydrogen," Phys. Rev. B 66, 035102 (2002) [spin-polarized GW]
  6. Sohrab Ismail-Beigi, "Truncation of periodic image interactions for confined systems," Phys. Rev. B 73, 233103 (2006) [slab and wire truncation]
  7. Jeffrey B. Neaton, Mark S. Hybertsen, and Steven G. Louie, "Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces," Phys. Rev. Lett. 97, 216405 (2006) [ICM] Erratum: p. 3, left col, last paragraph. Should be 1/2|z-z0| instead of 1/4|z-z0|.
  8. R. Haydock, "The recursive solution of the Schrödinger equation," Comput. Phys. Commun. 20, 11 (1980)
  9. Loren X. Benedict and Eric L. Shirley, "Ab initio calculation of ε2(ω) including the electron-hole interaction: Application to GaN and CaF2," Phys. Rev. B 59, 5441 (1999) [Haydock recursion in BSE]
  10. Georgy Samsonidze, Manish Jain, Jack Deslippe, Marvin L. Cohen, and Steven G. Louie, "Simple approximate physical orbitals for GW quasiparticle calculations," Phys. Rev. Lett. 107, 186404 (2011) [SAPO]
II. Review articles on the GW approximation and Bethe-Salpeter equation approaches
  1. Lars Hedin and Stig Lundqvist, "Effects of Electron-Electron and Electron-Phonon Interactions on the One-Electron States of Solids," Solid State Phys. 23, 1 (1970)
  2. Mark S. Hybertsen and Steven G. Louie, "Theory and Calculation of Quasiparticle Energies and Band Gaps," Comments on Cond. Mat. Phys. 13, 223 (1987)
  3. G. Strinati, "Application of the Green's functions method to the study of the optical properties of semiconductors," Riv. Nuovo Cimento 11, 1 (1988)
  4. Steven G. Louie, "Quasiparticle Theory of Electron Excitations in Solids," in Quantum Theory of Real Materials, eds. James R. Chelikowsky and Steven G. Louie, (Kluwer Press, Boston, 1996), p. 83
  5. Steven G. Louie, "First-Principles Theory of Electron Excitation Energies in Solids, Surfaces, and Defects," in Topics in Computational Materials Science, ed. Ching-Yao Fong (World Scientific, Singapore, 1998) p. 96
  6. F. Aryasetiawan and O. Gunnarsson, "The GW method," Rep. Prog. Phys. 61, 237 (1998)
  7. Lars Hedin, "On correlation effects in electron spectroscopies and the GW approximation," J. Phys.: Condens. Matter 11, R489 (1999)
  8. Wilfried G. Aulbur, Lars Jönsson, and John W. Wilkins, "Quasiparticle calculations in solids," Solid State Phys. 54, 1 (1999)
  9. Giovanni Onida, Lucia Reining, and Angel Rubio, "Electronic excitations: density-functional versus many-body Green's-function approaches," Rev. Mod. Phys. 74, 601 (2002)
  10. Steven G. Louie, "Predicting Materials and Properties: Theory of the Ground and Excited State," in Conceptual Foundations of Materials: A Standard Model for Ground- and Excited-State Properties, vol. eds. Steven G. Louie and Marvin L. Cohen (Elsevier, Amsterdam, 2006) p. 9
III. Papers using BerkeleyGW
  1. Mark S. Hybertsen and Steven G. Louie, "First Principles Theory of Quasiparticles: Calculation of Band Gaps in Semiconductors and Insulators," Phys. Rev. Lett. 55, 1418 (1985)
  2. Mark S. Hybertsen and Steven G. Louie, "Electron Correlation and the Band Gap in Ionic Crystals," Phys. Rev. B 32, 7005(R) (1985) [Erratum: Phys. Rev. B 35, 9308 (1987)]
  3. Mark S. Hybertsen and Steven G. Louie, "Many-body Calculation of Surface States: As on Ge(111)," Phys. Rev. Lett. 58, 1551 (1987)
  4. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Theory of Quasiparticle Energies in Alkali Metals," Phys. Rev. Lett. 59, 819 (1987)
  5. Steven G. Louie and Mark S. Hybertsen, "Theory of Quasiparticle Energies: Band Gaps and Excitation Spectra in Solids," Int. J. Quant. Chem.: Quant. Chem. Symp. 21, 31 (1987)
  6. Sheng Bai Zhang, David Tománek, Steven G. Louie, Marvin L. Cohen, and Mark S. Hybertsen, "Quasiparticle Calculation of Valence Band Offset of AlAs-GaAs(001)," Solid State Comm. 66, 585 (1988)
  7. Mark S. Hybertsen and Steven G. Louie, "Theory of Quasiparticle Surface States in Semiconductor Surfaces," Phys. Rev. B 38, 4033 (1988)
  8. Michael P. Surh, John E. Northrup, and Steven G. Louie, "Occupied Quasiparticle Bandwidth of Potassium," Phys. Rev. B 38, 5976 (1988)
  9. Xuejun Zhu, Stephen Fahy, and Steven G. Louie, "Ab Initio Calculation of Pressure Coefficients of Band Gaps of Silicon: Comparison of the Local-Density Approximation and Quasiparticle Results," Phys. Rev. B 39, 7840 (1989) [Erratum: Phys. Rev. B 40, 5821 (1989)]
  10. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Quasiparticle excitation spectrum for nearly-free-electron metals," Phys. Rev. B 39, 8198 (1989)
  11. Sheng Bai Zhang, David Tománek, Marvin L. Cohen, Steven G. Louie, and Mark S. Hybertsen, "Evaluation of Quasiparticle Energies for Semiconductors without Inversion Symmetry," Phys. Rev. B 40, 3162 (1989)
  12. Sheng Bai Zhang, Mark S. Hybertsen, Marvin L. Cohen, Steven G. Louie, and David Tománek, "Quasiparticle Band Gaps for Ultrathin GaAs/AlAs(001) Superlattices," Phys. Rev. Lett. 63, 1495 (1989)
  13. Xuejun Zhu, Sheng Bai Zhang, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle Interpretation of Photoemission Spectra and Optical Properties of GaAs(110)," Phys. Rev. Lett. 63, 2112 (1989)
  14. Sheng Bai Zhang, Marvin L. Cohen, Steven G. Louie, David Tománek, and Mark S. Hybertsen, "Quasiparticle Band Offset at the (001) Interface and Band Gaps in Ultrathin Superlattices of GaAs-AlAs Heterojunctions," Phys. Rev. B 41, 10058 (1990)
  15. Hélio Chacham, Xuejun Zhu, and Steven G. Louie, "Metal-Insulator Transition in Solid Xenon at High Pressures," Europhys. Lett. 14, 65 (1991)
  16. Hélio Chacham and Steven G. Louie, "Metallization of Solid Hydrogen at Megabar Pressures: A First-Principles Quasiparticle Study," Phys. Rev. Lett. 66, 64 (1991)
  17. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Many-Body Calculation of the Surface State Energies for Si(111)2×1," Phys. Rev. Lett. 66, 500 (1991)
  18. Michael P. Surh, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle Energies for Cubic BN, BP, and BAs," Phys. Rev. B 43, 9126 (1991)
  19. Xuejun Zhu and Steven G. Louie, "Quasiparticle Surface Band Structure and Photoelectric Threshold of Ge(111)-2×1," Phys. Rev. B 43, 12146(R) (1991)
  20. Xuejun Zhu and Steven G. Louie, "Quasiparticle Band Structure of Thirteen Semiconductors and Insulators," Phys. Rev. B 43, 14142 (1991)
  21. Michael P. Surh, Steven G. Louie, and Marvin L. Cohen, "Band Gaps of Diamond under Anisotropic Stress," Phys. Rev. B 45, 8239 (1992)
  22. Hélio Chacham, Xuejun Zhu, and Steven G. Louie, "Pressure-Induced Insulator-Metal Transitions in Solid Xenon and Hydrogen: A First-Principles Quasiparticle Study," Phys. Rev. B 46, 6688 (1992) [Erratum: Phys. Rev. B 48, 2025(E) (1993)]
  23. Eric L. Shirley, Xuejun Zhu, and Steven G. Louie, "Core-Polarization in Semiconductors: Effects on Quasiparticle Energies," Phys. Rev. Lett. 69, 2955 (1992)
  24. Eric L. Shirley and Steven G. Louie, "Electron Excitations in Solid C60: Energy Gap, Band Dispersions, and Effects of Orientational Disorder," Phys. Rev. Lett. 71, 133 (1993)
  25. Angel Rubio, Jennifer L. Corkill, Marvin L. Cohen, Eric L. Shirley, and Steven G. Louie, "Quasiparticle Band Structure of AlN and GaN," Phys. Rev. B 48, 11810 (1993)
  26. Steven G. Louie and Eric L. Shirley, "Electron Excitation Energies in Fullerites: Many-Electron and Molecular Orientational Effects," J. Phys. Chem. Solids 54, 1767 (1993)
  27. Xavier Blase, Xuejun Zhu, and Steven G. Louie, "Self-Energy Effects on the Surface State Energies of H-Si(111) 1×1," Phys. Rev. B 49, 4973 (1994)
  28. J. A. Carlisle, L. J. Terminello, A. V. Hamza, E. A. Hudson, Eric L. Shirley, F. J. Himpsel, D. A. Lapiano-Smith, J. J. Jia, T. A. Callcott, R. C. C. Perera, D. K. Shuh, Steven G. Louie, J. Stöhr, M. G. Samant, and D. L. Ederer, "Occupied and Unoccupied Orbitals of C60 and C70," Mol. Cryst. Liq. Cryst. 256, 819 (1994)
  29. Oleg Zakharov, Angel Rubio, Xavier Blase, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Band Structures of Six II-VI Compounds: ZnS, ZnSe, ZnTe, CdS, CdSe, and CdTe," Phys. Rev. B 50, 10780 (1994)
  30. Xavier Blase, Angel Rubio, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle band structure of bulk hexagonal boron nitride and related systems," Phys. Rev. B 51, 6868 (1995)
  31. Michael P. Surh, Hélio Chacham, and Steven G. Louie, "Quasiparticle Excitation Energies for the F-Center Defect in LiCl," Phys. Rev. B. 51, 7464 (1995)
  32. Eric L. Shirley and Steven G. Louie, "Photoemission and Optical Properties of C60 Fullerites," in Quantum Theory of Real Materials, eds. J.R. Chelikowsky and Steven G. Louie (Kluwer Press, Boston, 1996), p. 515.
  33. Balázs Králik, Eric K. Chang, and Steven G. Louie, "Structural Properties and Quasiparticle Band Structure of Zirconia," Phys. Rev. B 57, 7027 (1998)
  34. Michael Rohlfing and Steven G. Louie, "Electron-hole Excitations in Semiconductors and Insulators," Phys. Rev. Lett. 81, 2312 (1998)
  35. Michael Rohlfing and Steven G. Louie, "Optical Excitations in Conjugated Polymers," Phys. Rev. Lett. 82, 1959 (1999)
  36. Michael Rohlfing and Steven G. Louie, "Excitons and Optical Spectrum of the Si(111)-(2×1) Surface," Phys. Rev. Lett. 83, 856 (1999)
  37. Eric K. Chang, Michael Rohlfing, and Steven G. Louie, "Excitons and Optical Properties of Alpha-Quartz," Phys Rev. Lett. 85, 2613 (2000)
  38. Eric K. Chang, Michael Rohlfing, and Steven G. Louie, "First-Principles Study of Optical Excitations in Alpha-Quartz," in The Optical Properties of Materials, MRS Symp. Proceed. Vol. 579, eds. Eric L. Shirley, James R. Chelikowsky, Steven G. Louie, and Gérard Martinez (Materials Research Society, Warrendale, 2000), p. 3
  39. Peihong Zhang, Vincent H. Crespi, Eric K. Chang, Steven G. Louie, and Marvin L. Cohen, "Computational Design of Direct-Bandgap Semiconductors that Lattice-Match Silicon," Nature 409, 69 (2001)
  40. Jeffrey C. Grossman, Michael Rohlfing, Lubos Mitas, Steven G. Louie, and Marvin L. Cohen, "High Accuracy Many-Body Calculational Approaches for Excitations in Molecules," Phys. Rev. Lett. 86, 472 (2001)
  41. Gian-Marco Rignanese, Xavier Blase, and Steven G. Louie, "Quasiparticle Effects on Tunneling Currents: A Study of C2H4 Adsorbed on the Si(001)-(2×1) Surface," Phys. Rev. Lett. 86, 2110 (2001)
  42. Eric K. Chang, Xavier Blase, and Steven G. Louie, "Quasiparticle Band Structure of Lanthanum Hydride," Phys. Rev. B 64, 155108 (2001)
  43. Catalin D. Spataru, M. A. Cazalilla, Angel Rubio, Loren X. Benedict, Pedro M. Echenique, and Steven G. Louie, "Anomalous Quasiparticle Lifetime in Graphite: Band Structure Effects," Phys. Rev. Lett. 87, 246405 (2001)
  44. Je-Luen Li, Gian-Marco Rignanese, Eric K. Chang, Xavier Blase, and Steven G. Louie, "GW Study of the Metal-Insulator Transition of bcc Hydrogen," Phys. Rev. B 66, 035102 (2002)
  45. Weidong Luo, Sohrab Ismail-Beigi, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Band Structure of ZnS and ZnSe," Phys. Rev. B 66, 195215 (2002)
  46. Loren X. Benedict, Catalin D. Spataru, and Steven G. Louie, "Quasiparticle Properties of a Simple Metal at High Electron Temperatures," Phys. Rev. B 66, 085116 (2002)
  47. J. A. Alford, Mei-Yin Chou, Eric K. Chang, and Steven G. Louie, "First-principles Studies of Quasiparticle Band Structures of Cubic YH3 and LaH3," Phys. Rev. B 67, 125110 (2003)
  48. Murilo L. Tiago, John E. Northrup, and Steven G. Louie, "Ab initio calculation of the electronic and optical properties of solid pentacene," Phys. Rev. B 67, 11 5212 (2003)
  49. Sohrab Ismail-Beigi and Steven G. Louie, "Excited-State Forces within a First-Principles Green's Function Formalism," Phys. Rev. Lett. 90, 076401 (2003)
  50. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Excitonic effects and optical spectra of single-walled carbon nanotubes," Phys. Rev. Lett. 92, 077402 (2004)
  51. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Quasiparticle energies, excitonic effects and optical absorption spectra of small-diameter single-walled carbon nanotubes," Appl. Phys. A 78, 1129 (2004)
  52. Murilo L. Tiago, Sohrab Ismail-Beigi, and Steven G. Louie, "Effect of Semicore Orbitals on the Electronic Band Gaps of Si, Ge, and GaAs Within the GW Approximation," Phys. Rev. B 69, 125212 (2004)
  53. Catalin D. Spataru, Loren X. Benedict, and Steven G. Louie, "Ab Initio Calculation of Band-Gap Renormalization in Highly Excited GaAs," Phys. Rev. B 69, 205204 (2004)
  54. Murilo L. Tiago, Michael Rohlfing, and Steven G. Louie, "Bound Excitons and Optical Properties of Bulk Trans-Polyacetylene," Phys. Rev. B 70, 193204 (2004)
  55. Je-Luen Li, Gian-Marco Rignanese, and Steven G. Louie, "Quasiparticle Energy Bands of NiO in the GW Approximation," Phys. Rev B 71, 193102 (2005)
  56. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Excitonic Effects and Optical Spectra of Single-Walled Carbon Nanotubes," 27th Conference on the Physics of Semiconductors, AIP Conference Proceedings 772, 1061 (2005)
  57. Jeffrey B. Neaton, Koonghong Khoo, Catalin D. Spataru, and Steven G. Louie, "Electronic Transport and Optical Properties of Carbon Nanostructures from First Principles," Comput. Phys. Commun. 169, 1 (2005)
  58. Sohrab Ismail-Beigi and Steven G. Louie, "Self-Trapped Excitons in Silicon Dioxide: Mechanism and Properties," Phys. Rev. Lett. 95, 156401 (2005)
  59. Catalin D. Spataru, Sohrab Ismail-Beigi, Rodrigo B. Capaz, and Steven G. Louie, "Theory and Ab Initio Calculation of Radiative Lifetime of Excitons in Semiconducting Carbon Nanotubes," Phys. Rev. Lett. 95, 247402 (2005)
  60. Steven G. Louie and Angel Rubio, "Quasiparticle and Optical Properties of Solids and Nanostructures: The GW-BSE Approach," Handbook of Materials Modeling, ed. S. Yip (Springer, Dordrecht, The Netherlands, 2005), p. 215
  61. Cheol-Hwan Park, Catalin D. Spataru, and Steven G. Louie, "Excitons and Many-Electron Effects in the Optical Response of Single-Walled Boron Nitride Nanotubes," Phys. Rev. Lett. 96, 126105 (2006)
  62. Jeffrey B. Neaton, Mark S. Hybertsen, and Steven G. Louie, "Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces," Phys. Rev. Lett. 97, 216405 (2006)
  63. Su Ying Quek, Jeffrey B. Neaton, Mark S. Hybertsen, E. Kaxiras, and Steven G. Louie, "First-principles Studies of the Electronic Structure of Cyclopentene on Si(001): Density Functional Theory and GW Calculations," Phys. Status Solidi (b) 243, 2048 (2006)
  64. Rodrigo B. Capaz, Catalin D. Spataru, Sohrab Ismail-Beigi, and Steven G. Louie, "Diameter and Chirality Dependence of Exciton Properties in Carbon Nanotubes," Phys. Rev. B 74, 121401 (2006)
  65. Takashi Miyake, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Energy of Semicore d-electrons in ZnS: Combined LDA+U and GW approach," Phys. Rev. B 74, 245213 (2006)
  66. Li Yang, Catalin D. Spataru, Steven G. Louie, and Mei-Yin Chou, "Enhanced Electron-hole Interaction and Optical Absorption in a Silicon Nanowire," Phys. Rev. B 75, 201304(R) (2007)
  67. Li Yang, Cheol-Hwan Park, Young-Woo Son, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Energies and Band Gaps of Graphene Nanoribbons," Phys. Rev. Lett. 99, 186801 (2007)
  68. Li Yang, Marvin L. Cohen, and Steven G. Louie, "Excitonic Effects in the Optical Spectra of Graphene Nanoribbons," Nano Lett. 7, 3112 (2007)
  69. Feng Wang, David J. Cho, Brian Kessler, Jack Deslippe, P. James Schuck, Steven G. Louie, Alex Zettl, Tony F. Heinz, and Y. Ron Shen, "Observation of Excitons in One-Dimensional Metallic Single-Walled Carbon Nanotubes," Phys. Rev. Lett. 99, 227401 (2007)
  70. Su Ying Quek, Jeffrey B. Neaton, Mark S. Hybertsen, Efthimios Kaxiras, and Steven G. Louie, "Negative Differential Resistance in Transport through Organic Molecules on Silicon," Phys. Rev. Lett. 98, 066807 (2007)
  71. Catalin D. Spataru, Sohrab Ismail-Beigi, Rodrigo B. Capaz, and Steven G. Louie, "Quasiparticle and Excitonic Effects in the Optical Response of Nanotubes and Nanoribbons," in Carbon Nanotubes: Advanced Topics in the Synthesis, Structure, Properties and Applications, A. Jorio, M. S. Dresselhaus, G. Dresselhaus (eds.), Topics in Applied Physics 111 (Springer-Verlag, Heidelberg, Germany 2008), p. 195
  72. Jack Deslippe, Catalin D. Spataru, David Prendergast, and Steven G. Louie, "Bound excitons in metallic single-walled carbon nanotubes," Nano Lett. 7, 1626 (2007)
  73. Cheol-Hwan Park, Feliciano Giustino, Marvin L. Cohen, and Steven G. Louie, "Velocity Renormalization and Carrier Lifetime in Graphene from the Electron-Phonon Interaction," Phys. Rev. Lett. 99, 086804 (2007)
  74. Brad D. Malone, Jay D. Sau, and Marvin L. Cohen, "Ab initio survey of the electronic structure of tetrahedrally bonded phases of silicon," Phys. Rev. B 78, 035210 (2008)
  75. Jack Deslippe and Steven G. Louie, "Excitons and Many-electron Effects in the Optical Response of Carbon Nanotubes and Other One-dimensional Nanostructures," Proc. SPIE 6892, 68920U-1 (2008)
  76. Emmanouil Kioupakis, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "GW Quasiparticle Corrections to the LDA+U/GGA+U Electronic Structure of bcc Hydrogen," Phys. Rev. B 77, 155114 (2008)
  77. Jay D. Sau, Jeffrey B. Neaton, Hyoung Joon Choi, Steven G. Louie, and Marvin L. Cohen, "Electronic Energy Levels of Weakly Coupled Nanostructures: C60 Metal Interfaces," Phys. Rev. Lett. 101, 026804 (2008)
  78. Li Yang, Marvin L. Cohen, and Steven G. Louie, "Magnetic Edge-state Excitons in Zigzag Graphene Nanoribbons," Phys. Rev. Lett. 101, 186401 (2008)
  79. Cheol-Hwan Park, Feliciano Giustino, Jessica L. McChesney, Aaron Bostwick, Taisuke Ohta, Eli Rotenberg, Marvin L. Cohen, and Steven G. Louie, "Van Hove Singularity and Apparent Anisotropy in the Electron-phonon Interaction in Graphene," Phys. Rev. B 77, 113410 (2008)
  80. Cheol-Hwan Park, Feliciano Giustino, Marvin L. Cohen, and Steven G. Louie, "Electron-phonon Interactions in Graphene, Bilayer Graphene, and Graphite," Nano Lett. 8, 4229 (2008)
  81. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "First-principles Study of Electron Linewidths in Graphene," Phys. Rev. Lett. 102, 076803 (2009) [Erratum: Phys. Rev. Lett. 102, 189904(E) (2009)]
  82. Jack Deslippe, Mario Dipoppa, David Prendergast, M. V. O. Moutinho, Rodrigo B. Capaz, and Steven G. Louie, "Electron-hole Interaction in Carbon Nanotubes: Novel Screening and Exciton Excitation Spectra," Nano Lett. 9, 1330 (2009)
  83. Li Yang, Jack Deslippe, Cheol-Hwan Park, Marvin L. Cohen, and Steven G. Louie, "Excitonic effects on the optical response of graphene and bilayer graphene," Phys. Rev. Lett. 103, 186802 (2009)
  84. Chenggang Tao, J. Sun, X. Zhang, Ryan Yamachika, Daniel Wegner, Yasaman Bahri, Georgy Samsonidze, Marvin L. Cohen, Steven G. Louie, T. Don Tilley, Rachel A. Segalman, and Michael F. Crommie, "Spatial resolution of a type II heterojunction in a single bipolar molecule," Nano Lett. 9, 3963 (2009)
  85. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "Angle-resolved Photoemission Spectra of Graphene from First-principles," Nano Lett. 9, 4234 (2009)
  86. Emmanouil Kioupakis, Murilo L. Tiago, and Steven G. Louie, "Quasiparticle electronic structure of bismuth telluride in the GW approximation," Phys. Rev. B 82, 245203 (2010)
  87. Feliciano Giustino, Steven G. Louie, and Marvin L. Cohen, "Electron-phonon renormalization of the direct band gap of diamond," Phys. Rev. Lett. 105, 265501 (2010)
  88. Brad D. Malone, Steven G. Louie, and Marvin L. Cohen, "Electronic and optical properties of body-centered-tetragonal Si and Ge," Phys. Rev. B 81, 115201 (2010)
  89. Bi-Ching Shih, Yu Xue, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle band gap of ZnO: High accuracy from the conventional G0W0 approach," Phys. Rev. Lett. 105, 146401 (2010)
  90. Victor W. Brar, Sebastian Wickenburg, Melissa Panlasigui, Cheol-Hwan Park, Tim O. Wehling, Yuanbo Zhang, R. Decker, Caglar Girit, A. V. Balatsky, Steven G. Louie, Alex Zettl, and Michael F. Crommie, "Observation of Carrier-Density-Dependent Many-Body Effects in Graphene via Tunneling Spectroscopy," Phys. Rev. Lett. 104, 036805 (2010)
  91. G. S. Do, J. Kim, Seung-Hoon Jhi, Cheol-Hwan Park, Steven G. Louie, and Marvin L. Cohen, "Ab Initio Calculations of Pressure-Induced Structural Phase Transitions of GeTe," Phys. Rev. B 82, 054121 (2010)
  92. Li Yang, "First-principles study of the optical absorption spectra of electrically gated bilayer graphene," Phys. Rev. B 81, 155445 (2010)
  93. David A. Siegel, Cheol-Hwan Park, C. Hwang, Jack Deslippe, A. V. Federov, Steven G. Louie, and Alessandra Lanzara, "Many-body Interactions in Quasi-freestanding Graphene," Proc. Natl. Acad. Sci. U.S.A. 108, 11365 (2011)
  94. H. C. Hsueh, G. Y. Guo, and Steven G. Louie, "Excitonic Effects in the Optical Properties of a SiC Sheet and Nanotubes," Phys. Rev. B 84, 85404 (2011)
  95. Georgy Samsonidze, Manish Jain, Jack Deslippe, Marvin L. Cohen, and Steven G. Louie, "Simple approximate physical orbitals for GW quasiparticle calculations," Phys. Rev. Lett. 107, 186404 (2011)
  96. Georgy Samsonidze, Marvin L. Cohen, and Steven G. Louie, "Compensation-doped silicon for photovoltaic applications," Phys. Rev. B 84, 195201 (2011)
  97. Manish Jain, James R. Chelikowsky, and Steven G. Louie, "Quasiparticle Excitations and Charge Transition Levels of Oxygen Vacancies in Hafnia," Phys. Rev. Lett. 107, 216803 (2011)
  98. Manish Jain, James R. Chelikowsky, and Steven G. Louie, "Reliability of Hybrid Functionals in Predicting Band Gaps," Phys. Rev. Lett. 107, 216806 (2011)
  99. Isaac Tamblyn, Pierre Darancet, Su Ying Quek, Stanimir A. Bonev, and Jeffrey B. Neaton, "Electronic energy level alignment at metal-molecule interfaces with a GW approach," Phys. Rev. B 84, 201402(R) (2011)
  100. Li Yang, "Excitons in intrinsic and bilayer graphene," Phys Rev. B 83, 085405 (2011)
  101. Li Yang, "Excitonic Effects on Optical Absorption Spectra of Doped Graphene," Nano Lett. 11, 3844 (2011)
  102. Oleg V. Yazyev, Emmanouil Kioupakis, Joel E. Moore, and Steven G. Louie, "Quasiparticle effects in the bulk and surface-state bands of Bi2Se3 and Bi2Te3 topological insulators," Phys. Rev. B 85, 161101(R) (2012)
  103. Sahar Sharifzadeh, Ariel Biller, Leeor Kronik, and Jeffrey B. Neaton, "Quasiparticle and Optical Spectroscopy of the Organic Semiconductors Pentacene and PTCDA from First Principles," Phys. Rev. B 85, 125307 (2012)
  104. Jesse Noffsinger, Emmanouil Kioupakis, Chris G. Van de Walle, Steven G. Louie, and Marvin L. Cohen, "Phonon-Assisted Optical Absorption in Silicon from First Principles," Phys. Rev. Lett. 108, 167402 (2012)
  105. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "Inelastic Carrier Lifetime in Bilayer Graphene," Appl. Phys. Lett. 100, 032106 (2012)
  106. Kaihui Liu, Jack Deslippe, Fajun Xiao, Rodrigo B. Capaz, Xiaoping Hong, Shaul Aloni, Alex Zettl, Wenlong Wang, Xuedong Bai, Steven G. Louie, Enge Wang and Feng Wang, "A Periodic Table of Carbon Nanotube Optical Transitions," Nature Nanotech. 7, 325 (2012)
  107. Sangkook Choi, Jack Deslippe, Rodrigo B. Capaz, and Steven G. Louie, "An explicit formula for optical oscillator strength of excitons in semiconducting single-walled carbon nanotubes: family behavior", Nano Lett. 13, 54 (2012)
  108. Sahar Sharifzadeh, Isaac Tamblyn, Peter Doak, Pierre Darancet, and Jeffrey B. Neaton, "Quantitative Molecular Orbital Energies within a G0W0 Approximation", Eur. Phys. J. B 85, 323 (2012)
  109. Jack Deslippe, Georgy Samsonidze, Manish Jain, Marvin L. Cohen and Steven G. Louie, "Coulomb-hole summations and energies for GW calculations with limited number of empty orbitals: A modified static remainder approach", Phys. Rev. B 87, 165124 (2013)
  110. Brad D. Malone and Marvin L. Cohen, "Quasiparticle semiconductor band structures including spin-orbit interactions," J. Phys.: Condens. Matter 25, 105503 (2013)
  111. Diana Y. Qiu, Felipe H. da Jornada and Steven G. Louie, "Optical Spectrum of MoS2: Many-Body Effects and Diversity of Exciton States," Phys. Rev. Lett. 111, 216805 (2013)
  112. Georgy Samsonidze, Marvin L. Cohen, and Steven G. Louie, "First-principles study of quasiparticle energies of a bipolar molecule in a scanning tunneling microscope measurement," Comput. Mater. Sci. 91, 187 (2014)
  113. Georgy Samsonidze, Filipe J. Ribeiro, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle and optical properties of polythiophene-derived polymers," Phys. Rev. B 90, 035123 (2014)
  114. Manish Jain, Jack Deslippe, Georgy Samsonidze, Marvin L. Cohen, James R. Chelikowsky, and Steven G. Louie, "Improved quasiparticle wave functions and mean field for G0W0 calculations: Initialization with the COHSEX operator," Phys. Rev. B 90, 115148 (2014)
  115. Georgy Samsonidze, Cheol-Hwan Park, and Boris Kozinsky, "Insights and challenges of applying the GW method to transition metal oxides," J. Phys.: Condens. Matter 26, 475501 (2014)
  116. Dylan Bayerl and Emmanouil Kioupakis, "Visible-Wavelength Polarized-Light Emission with Small-Diameter InN Nanowires," Nano Lett. 14, 3709 (2014)
  117. M. Gerosa, C. E. Bottani, L. Caramella, G. Onida, C. Di Valentin, and G. Pacchioni, "Electronic structure and phase stability of oxide semiconductors: Performance of dielectric-dependent hybrid functional DFT, benchmarked against GW band structure calculations and experiments", Phys. Rev. B 91, 155201 (2015)
  118. Guangsha Shi and Emmanouil Kioupakis, "Electronic and Optical Properties of Nanoporous Silicon for Solar-Cell Applications," ACS Photonics 2, 208 (2015)
  119. Huashan Li, David A. Strubbe, and Jeffrey C. Grossman, "Functionalized Graphene Superlattice as a Single-Sheet Solar Cell," Adv. Funct. Mater. 25, 5199-5205 (2015)

config/README

# Information about how to set the various options here. # Ideally you can use a file already created for your platform in this directory. # Otherwise, you can work from the one most similar that is here. # Select the Fortran compiler you are using. # if you have a different one than these, modifications in Common/compiler.h # and Common/common-rules.mk will be necessary. COMPFLAG = -D{INTEL, PGI, GNU, PATH, XLF, G95, ABSOFT, NAG, OPEN64, SUN, CRAY} # Use -DMPI to compile Fortran in parallel with MPI. Otherwise is serial. # Add -DOMP to compile with OpenMP support. Also add appropriate compiler-dependent flag to F90free: # ifort, sunf90, absoft, pathscale, Open64: -openmp. PGI: -mp=nonuma. gfortran: -fopenmp. XLF: -qsmp=omp. # crayftn: on by default (to turn off use -h noomp). g95 and NAG do not support OpenMP. PARAFLAG = -DMPI # -DUSESCALAPACK enables usage of ScaLAPACK (required in parallel for BSE). # -DUSEESSL uses ESSL instead of LAPACK in some parts of the code. # -DUNPACKED uses unpacked rather than packed representation of the Hamiltonian # in EPM. Packed LAPACK operations give bad results eventually in Si-EPM kernel 'max x' # test for ACML, Cray LibSci, and MKL sometimes. # -DUSEFFTW3 uses fftw3 instead of fftw2, which is recommended for better performance, and enables threading. # -DHDF5 enables usage of HDF5 for writing epsmat and bsemat files. The produced files will be # eps0mat.h5, epsmat.h5 and bsemat.h5 and are used in place of eps0mat, epsmat, bsedmat, bsexmat # (the latter two are combined in one .h5 file). # Using -DHDF5 gives you substantially better IO performance in many cases by taking advantage # of HDF5's parallel IO options and other options. However, you must have the HDF5 libraries # installed on your system and define HDF5LIB and HDF5INCLUDE below. MATHFLAG = -DUSESCALAPACK -DUSEESSL -DUNPACKED -DHDF5 # For Fortran and C++. -DDEBUG enables extra checking. -DVERBOSE is an internal # flag, and is equivalent to running all codes with the maximum verbosity level. # Don't use the -DVERBOSE option, unless a developer told you to. The -DDEBUG # option makes extra memory checks, and slows down the code by up to ~20%. # Only use these flags if you need to develop or debug BerkeleyGW. # The output will be much more verbose, and the code will slow down by ~20%. DEBUGFLAG = -DDEBUG -DVERBOSE # Same, but for C and C++. C_DEBUGFLAG = -DDEBUG -DVERBOSE # Command for the preprocessor. -C (and not -ansi) should generally be used. # add -P if the Fortran compiler will not accept indication of line numbers. # Use gcc's (often in /lib/cpp) or a C compiler (even mpicc) with "-E". Some need "-x c" as well. FCPP = cpp -C # Fortran compiler and its flags for F90 and f90 files (free source form) # see above at PARAFLAG regarding flags for OpenMP. # With -DOMP and openmp flags here, you will get threaded BerkeleyGW. # Without -DOMP, but with openmp flags here, is appropriate for just using threaded libraries. # Sometimes, flags such as -fno-second-underscore or -assume 2underscores may be necessary # to make linking succeed against C libraries such as FFTW, depending on what compiler built them. F90free = {mpif90, mpiifort, ftn, ifort, pgf90, gfortran, ...} # Fortran compiler and any flag(s) required for linking LINK = {mpif90, mpiifort, ftn, ifort, pgf90, gfortran, ...} # Fortran optimization flags. The levels below will generally work. FOPTS = {-fast, -O3} # Fortran optimization flags for epsilon_main and sigma_main which can have # trouble in high optimization due to their long length. If below does not # work, try -O2. FNOOPTS = $(FOPTS) # Fortran compiler flag to specify location where module should be created. # different for each compiler, refer to examples. MOD_OPT = # Fortran compiler flag to specify where to look for modules. INCFLAG = -I # Use this to compile C++ in parallel with MPI. Leave blank for serial. # MPICH, MVAPICH, Intel MPI require also -DMPICH_IGNORE_CXX_SEEK, or an error may occur such as: # "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h" C_PARAFLAG = -DPARA # C++ compiling command and any needed flags CC_COMP = {mpiCC, mpicxx, mpiicpc, CC, icpc, pgCC, g++, ...} # C compiling command and any needed flags C_COMP = {mpicc, mpiicc, cc, icc, pgcc, gcc, ...} # C/C++ link command and any needed flags C_LINK = {mpiCC, mpicxx, mpiicpc, CC, icpc, pgCC, g++, ...} # C/C++ optimization flags # Note: for Intel compilers, it is equivalent to use icc or icpc on C++ files. C_OPTS = -fast # command to remove, for make clean REMOVE = /bin/rm -f # command for making archives (.a). Default is /usr/bin/ar. # Usually that is fine and AR does not need to be specified, but # to do interprocedural optimizations (IPO) with ifort, you need xiar instead. #AR = /usr/bin/env xiar # Math Libraries # path for FFTW library, used in lines below FFTWPATH = # link line for FFTW2 library. Sometimes needs to be -ldfftw FFTWLIB = -L$(FFTWPATH)/lib -lfftw # link line for FFTW3 library, if -DUSEFFTW3 is used. Including fftw_omp allows threaded run. # Note: To use FFTW3 from MKL, do not link the fftw3xf interfaces. FFTWLIB = -L$(FFTWPATH)/lib {-lfftw3_omp} -lfftw3 # FFTW2 requires include file fftw_f77.i; # Sometimes supercomputer installations will not have it. # If not, find it online and copy it: e.g. http://www.fifi.org/doc/fftw-dev/fortran/fftw_f77.i # FFTW3 requires include file fftw3.f03 instead. FFTWINCLUDE = $(FFTWPATH)/include # Different styles will apply depending on the package used. # Must provide BLAS as well as LAPACK: some packages will do this in one library file, # others will not. See examples in this directory for how to link with MKL, ACML, # ATLAS, Ubuntu packages, etc. For MKL, if you will use ScaLAPACK, it is most # convenient to include BLACS here too. For further info on linking with MKL, see # the link-line advisor at http://software.intel.com/sites/products/mkl/ LAPACKLIB = # Specify below if you have -DUSESCALAPACK in MATHFLAG. # BLACS must be provided here too, if it is not provided in LAPACKLIB above. See # examples in this directory for different packages, as with LAPACKLIB. Note that # you may have problems if ScaLAPACK was not built with the same LAPACK used above. SCALAPACKLIB = # Specify below if you have -DHDF5 in MATHFLAG. # If compiling in parallel, you must have HDF5 compiled with parallel support or linking will fail. # Path as below should generally work. Sometimes -lsz too, or static linkage, might be required. # Note that "-lz" is not from HDF5, but its dependency zlib. # libdl may be required on your system even when linking static HDF5 due to plugin support in 1.8.11 and higher HDF5PATH = HDF5INCLUDE = $(HDF5PATH)/include HDF5LIB = -L$(HDF5PATH)/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lz # Flags for performance profiling with an external tool such as IPM on NERSC PERFORMANCE = # Command to submit testsuite job script from testsuite directory. # qsub is for PBS. If no scheduler, put make check-parallel here. # In serial, delete this line. TESTSCRIPT = qsub {architecture}.scr

testsuite/README

BerkeleyGW testsuite David Strubbe 2009-2011 == Running tests == * To run the testsuite in serial, type "make check" in this directory or the main directory. "make check-save" will do the same, but retain the working directories for debugging. * To run in parallel without a scheduler, you can just use "make check-parallel" if you do not have a scheduler (e.g. PBS). Set environment variable SAVETESTDIRS=yes to save working directories. The tests use 4 cores, so be sure that at least that many are available, or use BGW_TEST_MPI_NPROCS (see below). * To run in parallel with a scheduler, type "make check-jobscript" or "make check-jobscript-save", which will execute the job script for the machine you are using, as specified in arch.mk by the line TESTSCRIPT. See example job scripts for various machines in this directory called *.scr. The tests use 4 cores, so be sure to request at least that many in the job script, or use BGW_TEST_MPI_NPROCS (see below). * Environment variables: - TEMPDIRPATH: sets the scratch directory where temporary working directories will be created. Default is /tmp, but on some machines you may not have permission to write there. - MPIEXEC: sets the command for parallel runs. Default is `which mpiexec`. Note that mpiexec and mpirun are generally equivalent (except for Intel MPI, in which case mpirun is recommended). Set this if you are using a different command such as 'ibrun' (SGE parallel environment), 'runjob' (BlueGene), or 'aprun' (Cray), if you need to use a different mpiexec than the one in your path, or if some options need to be appended to the command. Depending on the value of this variable, three styles of command line are used: ibrun, runjob, and mpirun/aprun. - BGW_TEST_MPI_NPROCS: set to overrule the number of processors listed in the test files. Useful for testing correctness of parallelization, if you don't have 4 cores, or to run the testsuite faster with more cores. [- BGW_TEST_NPROCS: deprecated, same as BGW_TEST_MPI_NPROCS, provided for compatibility with versions 1.0.x.] - MACHINELIST: if set, will be added to command line for MPI runs. This is needed in some MPI implementations. - EXEC: if set, will be added before name of executable. Used to run code through valgrind. * To run just one test, in its directory, run "../run_regression_test.pl [-s] [-p] -D ../../bin -f [testname].test". Include the -s flag to run in serial; otherwise it will be in parallel. Include the -p flag to preserve the working directory. Contents: (1) run_testsuite.sh -- this script runs tests from filenames ending in *.test in this directory. (2) run_regression_test.pl -- called from run_testsuite.sh for each individual test. (3) *.scr -- job scripts for running the testsuite on various parallel machines. (4) interactive*.sh -- scripts to run in parallel, in interactive mode. You have to follow the instructions in the script, not just run it. (5) queue_monitor.pl -- a Perl script for parallel tests with a SLURM or PBS scheduler, which submits a job and monitors the queue to see what happens. Used by the BuildBot. (6) test directories. (7) fix_testsuite.py -- (for developers) can be used to create or update match reference values in test files. (8) no_hires.sh -- Some clusters will not have the Perl package Time::HiRes installed which is needed for timing in run_regression_test.pl. You can just deactivate the usage with this script. (9) buildbot_query.pl -- (for developers) can be used to find the range of values obtained on the buildslaves for a particular match, to set values in the test files. == Writing tests == The test files consist of lines beginning with one of a set of tags, parsed by the Perl script. Comment lines beginning with '#' will be ignored. Test : title Write a title to output to identify the test. Should be the first tag in the file. Banner : text Write a heading in a box to identify a specific part of a test. Helpful when input files are generated by sed and do not have a distinct name. Enabled : Yes/No If Yes, will be run; if No, will not be run. Use to turn off a test without deleting it from the repository. Should be the second tag in the file. TestGroups : group-name [group-name2 [...]] The run_testsuite.sh script can be run with argument "-g" and a list of groups. Then tests will only be run if there is a match between the argument list and the list in TestGroups. Examples of groups that could be used: parallel, serial, long. [This tag is actually read by run_testsuite.sh rather than run_regression_test.pl.] Executable : program.x Name of executable to be run (path is bin directory). Persists for multiple runs, until next Executable tag. Processors : integer Number of processors to use. Ignored if mpiexec is not available. May not exceed the number in the reservation in the job scripts. Set to special value "serial" to run without mpiexec. Command : shell-command Specify a shell command, which will be executed in the working directory. Useful for renaming log files that would be overwritten by a subsequent run, or preprocessing input files by sed or other utilities (after putting in working directory with Copy). Copy : file.in [file_newname.in] Copy a file from test directory to run directory. If new name is not supplied, original name will be used. Useful if you want to sed a file before it is run. Unpack : data.tar.gz The file data.tar.gz in the test directory will have "tar xzf" run on it, with resulting files going to the working directory. Output : file.out Output will be piped into the file named here, in the working directory. Arguments : arg1 arg2 The current Executable will be executed (in serial) with the text given here as command-line argument(s). No files will be copied to working directory. Use redirection with ">" to capture the output if necessary. Input : file.in [file_newname.in/PIPE/CMDLINE/NONE/NOCOPY] The file named here will be copied from the test directory to the working directory, for use as input (unless NOCOPY is specified). If it is followed by "PIPE", the file will be piped into the executable. If it is followed by "CMDLINE", the file will be given as a command-line argument to the executable. If it is followed by "NONE", no file will be copied (useful if an input file was already generated by sed in the working directory). If it is followed by another name, the file's name in the working directory will be the new name. This tag causes actual execution of the run that has been set up by previous tags. Precision : 1e-5 A floating point number, the tolerance for testing whether a match has passed or failed. Persists until next Precision tag. Default is 1e-4. match ; name ; COMMAND(..); reference-value Extracts a calculated number from a run and tests it against the reference value. The name is an identifier printed to output. The number is extracted as the standard output from the listed COMMAND, which is one of this set: . GREP(filename, 'search-text', field, offset) Finds the first line in file containing 'search-text' (which MAY NOT contain a comma), and returns the specified field of that line. "Field" is meant in the sense used by 'awk', i.e. the line is parsed into white-space separated groups, indexed starting with 1. The optional 'offset' directs the use of the Mth line after the line containing 'search-text'. No offset is equivalent to offset = 0. This is the most robust of the commands and should be used when possible in preference to the others. . SIZE(filename) Returns the size of the specified file via 'ls -lt'. Useful for binary files whose contents cannot easily be checked. . LINE(filename, line, field) Returns the specified field of the specified line number from the file. Use GREP instead if possible. . SHELL(shell-command) The result is the standard output of the listed command. Deprecated; use GREP or LINE unless absolutely necessary. STOP TEST For debugging purposes, to halt test after the part you are studying has run.

library/README

================================================================================ BerkeleyGW library ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004) -------------------------------------------------------------------------------- To build other codes with BerkeleyGW output support, type 'make library' to create libBGW_wfn.a and wfn_rho_vxc_io_m.mod (and dependent modules), and then compile with -I library/ and link library/libBGW_wfn.a with the other code. An m4 macro for configure scripts is provided in this directory, for use in linking to this library. Codes linking the library should 'use' the module 'wfn_rho_vxc_io_m'. To generate real wavefunctions, a Gram-Schmidt process should be used. The appropriate parallelization scheme etc. will be dependent on the code, and cannot be easily handled in a general manner here, but examples can be found in MeanField/SIESTA/real.f90 and MeanField/ESPRESSO/pw2bgw.f90 (routine real_wfng).

examples/README

================================================================================ BerkeleyGW Examples ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. -------------------------------------------------------------------------------- This folder contains a set of example calculations for BerkeleyGW 1.2. The mean-field portion of the examples may be done with the Empirical Pseudopotential Method (EPM), or ab intio DFT, using the Quantum ESPRESSO, PARATEC, or ABINIT codes. Other mean-field codes, such as Octopus and PARSEC, are also supported, but we don't have examples for them at this point. The examples contained here are organized according to the mean-field starting point: 1. Example under the "DFT" folder, use ab initio DFT as the starting mean-field picture for our GW and Bethe-Salpeter equation (BSE) calculations. You must have either PARATEC, Quantum ESPRESSO, or ABINIT for run these examples. Required pseudopotentials are stored in DFT/pseudos. 2. Examples under the "EPM" folder use the Empirical Pseudopotential Method (EPM), and you won't need any external mean-field code to run these examples. Calculations in these folders are much shorter to run, but are probably of less Each of these directories contain a number of subdirectories, each of them containing a different example and a README file with the instructions how to run each examples and suggestion on the number of processors to use. Before you run anything, note that YOU MUST MODIFY ALL SCRIPTS in this folder to set the appropriate path to BerkeleyGW (eg: $HOME/GW), your parallel job launching command (eg: mpirun), and parallel submission flags (eg: "#SLURM ..."). Tutorial -------- The idea behind these examples is to provide a working set of input files and reference output files for several calculations that span a range of relevant materials. However, for a more pedagogical introduction to BerkeleyGW, we suggest you first try to run our tutorials that are designed for our yearly BerkeleyGW workshops, available at: https://sites.google.com/site/berkeleygw2015/home Note for ABINIT --------------- Our ABINIT wrapper is still experimental, and not all examples have been ported to use ABINIT. Note for Quantum ESPRESSO ------------------------- Quantum ESPRESSO examples are compatible with Quantum ESPRESSO 5.0 and later versions. If you want to run them with Quantum ESPRESSO 4.3.2 or earlier version, you should modify the input files for pw.x, and change "calculation = 'bands'" to "calculation = 'nscf'" and "CELL_PARAMETERS" to "CELL_PARAMETERS cubic". Basic examples -------------- - silicon: a bulk semiconductor. You should start here! - Includes PREBUILT tarball of DFT inputs from PARATEC. - Includes ref directories containing sample output from ESPRESSO and BerkeleyGW steps. - Available for EPM as well as DFT. - Shows how to use Wannier90 and sig2wan.x to obtain a GW bandstructure by interpolation (optional step). - Shows how to use inteqp to obtain a GW bandstructure by interpolation. - GaAs: similar to silicon example. Runs slightly faster. - sodium: a bulk metal - swcnt_5-5: (5,5) single-walled carbon nanotube, a metallic 1D system - swcnt_8-0: (8,0) single-walled carbon nanotube, a semiconducting 1D system - Has runs of plotxct with visualization by volume.py and surface.x. - CO: a small molecule - benzene: a slightly larger molecule - Includes run of gsphere.py and SIESTA. Advanced examples ----------------- These examples demonstrate how to use advanced features of the code, and they are not as tidy as the other examples. You are expected to modify submission - Si2_sapo: another silicon example - Shows how to perform iterative Davidson diagonalization in SAPO, - requires pw2bgw with write_vscg capability as in espresso-5.0.2. - Zn2O2: a bulk semiconductor - Includes ref directories containing sample output from ESPRESSO and BerkeleyGW steps. - Shows how to use inteqp to obtain a GW bandstructure by interpolation. - Shows how to perform iterative Davidson diagonalization in SAPO, requires pw2bgw with write_vscg capability as in espresso-5.0.2. - Shows how to use valence only charge density in the Generalized Plasmon Pole model, requires pw2bgw with calc_rhog capability as in espresso-5.0.2. Other examples --------------- - Make sure you visit the tutorials presented during the BerkeleyGW workshops: https://sites.google.com/site/berkeleygw2015/home - The testsuite runs may also be consulted, although they are not realistic calculations. - There are also examples in the Visual directory for the scripts there.

MeanField

MeanField/README

================================================================================ BerkeleyGW: MeanField wrappers and utilities ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. -------------------------------------------------------------------------------- Description: BerkeleyGW uses a mean-field starting point, typically from DFT. Currently, BerkeleyGW supports two plane-wave DFT codes, PARATEC and Quantum ESPRESSO; one localized-orbital DFT code, SIESTA; and two real-space codes, Octopus and PARSEC. You can find details on how to use BerkeleyGW with these codes in their respective directories. For testing purposes and for crude calculations of large systems, BerkeleyGW can be executed on top of the empirical pseudopotential plane-wave code. See MeanField/EPM for details. There is a tool for generating large numbers of unoccupied orbitals (approximate from plane waves or exact by iterative diagonalization). It is located in MeanField/SAPO. You can find a simple code for computing the Coulomb integral within an image-charge model in MeanField/ICM. -------------------------------------------------------------------------------- Tricks and hints: 1. Vxc0 Vxc0 is the G=0 component of the exchange-correlation potential Vxc. Vxc0 is added to the eigenvalues in the wavefunction files produced by PARATEC and ESPRESSO. Vxc0 is also included in the VXC and vxc.dat files produced by PARATEC and ESPRESSO (the VXC file contains Vxc(G) and the vxc.dat file contains matrix elements of Vxc). The two Vxc0 terms cancel out when calculating the quasiparticle corrections in the Sigma code. 2. Vacuum level To correct the DFT eigenvalues for the vacuum level take the average of the electrostatic potential on the faces of the unit cell in the non-periodic directions and subtract it from the DFT eigenvalues. The electrostatic potential is defined as Velec = Vbare + Vhartree, while the total potential is Vtot = Vbare + Vhartree + Vxc, hence Vtot contains Vxc0 and Velec does not. The average of Velec is fed into the Sigma code using keywords avgpot and avgpot_outer. The potentials can be generated with PARATEC and ESPRESSO. In PARATEC, use elecplot for Velec or potplot for Vtot, then convert from a3dr to cube using the Visual/volume.py script. In ESPRESSO, use iflag=3, output_format=6, and plot_num=11 for Velec or plot_num=1 for Vtot. The averaging is done with the Visual/average.py script. 3. Unit cell size If you truncate the Coulomb interaction, make sure that the size of the unit cell in non-periodic directions is at least two times larger than the size of the charge distribution. This is needed to avoid spurious interactions between periodic replicas but at the same time not to alter interactions within the same unit cell. Run Visual/surface.x to plot an isosurface that contains 99% of the charge density (see Visual/README for instructions on how to do this). The code will print the size of the box that contains the isosurface to stdout. Multiply the box dimensions in non-periodic directions by two to get the minimum size of the unit cell. 4. Inversion symmetry When using the real flavor of the code, make sure the inversion symmetry has no associated fractional translation (if it does, shift the coordinate origin). Otherwise WFN, VXC, RHO (and VSC in SAPO) have non-vanishing imaginary parts which are simply dropped in the real flavor of the code. This won't do any good to your calculation...

ESPRESSO

MeanField/ESPRESSO/README

Quantum ESPRESSO is available for download at http://www.quantum-espresso.org/ The interface between Quantum ESPRESSO and BerkeleyGW consists of three programs, kgrid.x, pw2bgw.x and bgw2pw.x. kgrid.x is compiled with BerkeleyGW package and pw2bgw.x and bgw2pw.x are compiled with Quantum ESPRESSO. Files for versions 4.3.2, 5.0.x, and 5.1.x are supplied here. Starting with version 5.0, compatible files of pw2bgw.f90 and bgw2pw.f90 are distributed with Quantum ESPRESSO. If you are using espresso-5.1, apply a patch following the instructions in BerkeleyGW/MeanField/ESPRESSO/version-5.1/README_patch. Alternatively, you can use BerkeleyGW/MeanField/ESPRESSO/version-5.1/pw2bgw.f90 (rather than espresso-5.1/PP/src/pw2bgw.f90), which includes a bugfix to the problem of an immediate segmentation fault or error saying 'MPI_Comm_rank: Invalid communicator'. To use: cp BerkeleyGW/MeanField/ESPRESSO/version-5.1/pw2bgw.f90 espresso-5.1/PP/src/ Then 'make pp' in espresso. This seems to happen for MPICH and MVAPICH (and probably the related IntelMPI) but not OpenMPI, but the updated version should work in all cases. This is fixed in espresso-5.1.1 and later versions. The development versions of pw2bgw.f90 and bgw2pw.f90 are available from Quantum ESPRESSO trunk. Quantum ESPRESSO allows anonymous checkouts of its source code. Use the command below and use 'anonymous' as the username and a blank password to checkout the code: svn checkout http://qeforge.qe-forge.org/svn/q-e/trunk/espresso You can find more details about Quantum ESPRESSO svn on this website: http://www.qe-forge.org/gf/project/q-e/scmsvn/ -------------------------------------------------------------------------------- kgrid.x pw.x can automatically generate a uniform grid of k-points, either unshifted or shifted by half a grid step (Monkhorst-Pack grid), and reduce it to the irreducible wedge of the Brillouin Zone with the symmetries of the point group of the Bravais lattice and optionally with time-reversal symmetry. The same functionality (and more) is provided by kgrid.x in this directory. Additionally, kgrid.x can use the symmetries of the space group of the crystal instead of the symmetries of the point group of Bravais lattice, which is needed for BerkeleyGW. kgrid.x is not limited to the unshifted/half-step shifted Monkhorst-Pack grids. It can generate an asymmetrically shifted fine grid used to improve the convergence in absorption calculations. Also, kgrid.x can generate a grid of k-points with a small q-shift used in Epsilon calculation to avoid the divergence of the Coulomb interaction. The list of k-points generated by kgrid.x must be manually added to the input file of pw.x. Note that time-reversal symmetry should NOT be used for BerkeleyGW (noinv = .false. if generating the k-grid in pw.x), unless the utility wfn_time_reversal.x is run afterward. The format of the input file for kgrid.x (along with an example for Si) is found in kgrid.inp. See also more information in the header of kgrid.f90. You can find the input files for kgrid.x in examples/DFT in the ESPRESSO subdirectories of each example. -------------------------------------------------------------------------------- data-file2kgrid.py Parses the atomic positions and FFT grid from a Quantum Espresso data-file.xml file and creates the input file kgrid.inp for the kgrid.x utility. All options to kgrid.x -- such as number of k-points, k-shift, and k-grid -- are read as optional command-line arguments to data-file2kgrid.py. Type data-file2kgrid.py --help for a list of possible options. -------------------------------------------------------------------------------- pw2bgw.x Converts the output files produced by pw.x to the input files for BerkeleyGW. You cannot use USPP, PAW, or spinors in a pw.x run for BerkeleyGW. You cannot use "K_POINTS gamma" in a pw.x run for BerkeleyGW. Use "K_POINTS { tpiba | automatic | crystal }" even for the Gamma-point calculation. The format of the input file for pw2bgw.x is described in files MeanField/ESPRESSO/version-4.3.2/pw2bgw.inp, MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.html (copy of espresso-5.1/PP/Doc/INPUT_pw2bgw.html), which is generated from MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.def, and MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.html (copy of espresso-5.0.3/PP/Doc/INPUT_pw2bgw.html), which is generated from MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.def. You can find the input files for pw2bgw.x in examples/DFT in the ESPRESSO subdirectories of each example. Version 4.3.2 and earlier: It is recommended to run a pw.x "nscf" calculation with "K_POINTS crystal" and a list of k-points produced by kgrid.x. Sometimes pw.x generates additional k-points in a "nscf" run with an explicit list of k-points. If this is the case for your calculation, there are several ways to go around this problem: * Apply the patch provided with BerkeleyGW. It will prevent pw.x from generating additional k-points if they are provided explicitly, and take care of the normalization of the weights of k-points in a "bands" calculation. * Do not specify the atomic positions in the input file of kgrid.x (set number of atoms = 0). Then pw.x will generate additional k-points which are the correct ones. Also set noinv = .true. in the input file of pw.x if time-reversal symmetry was not used in kgrid.x. * Run a pw.x "bands" calculation instead of "nscf". In this case you have to explicitly specify the occupations in the input file of pw2bgw.x (note that this only works for insulators) and to normalize the weights of k-points to one in the input file of pw.x. Version 5.0 and later: It is recommended to run a pw.x "bands" calculation with "K_POINTS crystal" and a list of k-points produced by kgrid.x. You can also run a pw.x "nscf" calculation instead of "bands", but in this case pw.x may generate more k-points than provided in the input file of pw.x. If this is the case for your calculation you will get errors in BerkeleyGW. -------------------------------------------------------------------------------- bgw2pw.x Converts BerkeleyGW WFN and RHO files to the format of pw.x. This can be useful, for example, if you generate the plane waves on top of the valence bands and want to diagonalize them in pw.x. Look at the documentation for SAPO code in BerkeleyGW for more information. Another possible use is to convert between different versions of pw.x. bgw2pw.x reads common parameters from file prefix.save/data-file.xml and writes files prefix.save/charge-density.dat (charge density in R-space), prefix.save/gvectors.dat (G-vectors for charge density and potential), prefix.save/K$n/eigenval.xml (eigenvalues and occupations for nth k-point), prefix.save/K$n/evc.dat (wavefunctions in G-space for nth k-point), and prefix.save/K$n/gkvectors.dat (G-vectors for nth k-point). You must have prefix.save/K$n/eigenval.xml files present, or an error will occur, even though their contents will not be used and will be overwritten. The best is to run a pw.x calculation and use its prefix.save, e.g. from scf and then get unoccupied bands from bgw2pw.x. bgw2pw.x doesn't create restart files, so you cannot use restart_mode = 'restart' for a subsequent pw.x run. Instead, use startingwfc = 'file'. Make sure wf_collect = .true. and there are no prefix.wfc* files present. Also, the pw.x run that generated the prefix.save directory originally must have wf_collect = .true. also, for the appropriate links to the K$n files to be present. bgw2pw.x doesn't modify file prefix.save/data-file.xml so make changes to this file manually. For example, you will need to change the NUMBER_OF_BANDS and NUMBER_OF_PROCESSORS tags (as well as per pool and per image) to make sure these match the number of bands from the WFN file, as well as the number of processors you will use in a subsequent run. The format of the input file for bgw2pw.x is described in files MeanField/ESPRESSO/version-4.3.2/bgw2pw.inp, MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.html (copy of espresso-5.1/PP/Doc/INPUT_bgw2pw.html), which is generated from MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.def, and MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.html (copy of espresso-5.0.3/PP/Doc/INPUT_bgw2pw.html), which is generated from MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.def. -------------------------------------------------------------------------------- Notes on running pw.x Sometimes pw.x crashes when trying to generate a LARGE number of unoccupied states needed for GW calculations. The error messages may refer to "Cholesky decomposition" or "diagonalization". If you run into this problem try one of the following workarounds, or a combination of them: 1) Increase ecutwfc. Iterative diagonalization becomes inefficient and unstable with increasing the ratio of the number of states to the size of the Hamiltonian. Increasing ecutwfc will decrease this ratio at the cost of computation time. 2) Split the calculation over k-points. If one k-point fails, it won't affect the other k-points. You can merge the final wavefunction file using MeanField/Utilities/wfnmerge.x after running pw2bgw.x for each k-point. 3) Start with random instead of randomized atomic wavefunctions. For this use the following parameter in the input file of pw.x: startingwfc = 'random' 4) Split the diagonalization into several steps alternating between different diagonalization schemes. For example, use the following parameters in the input files for consequent runs of pw.x: 1st run: conv_thr = 1.0d-2 diagonalization = 'david' 2nd run: conv_thr = 1.0d-4 diagonalization = 'cg' startingwfc = 'file' 3rd run: conv_thr = 1.0d-6 diagonalization = 'david' startingwfc = 'file' etc. 5) Run pw.x with "-ndiag 1". Often serial diagonalization is more stable than the parallel one, and the time and memory overhead is bearable in most cases. 6) Compile pw.x without "-D__SCALAPACK" in DFLAGS in make.sys for using a custom distributed-memory diagonalization instead of ScaLAPACK. This is useful to check if the problem is caused by improper installation of ScaLAPACK. Note that you will have to explicitly specify ndiag, e.g. "mpirun -np 24 pw.x -ndiag 16 -in prefix.in > prefix.out", because pw.x only sets ndiag automatically in case of ScaLAPACK. 7) Last but not least, perform iterative diagonalization in SAPO instead of using pw.x, see examples/DFT/Si2_sapo for details. Finally, it is recommended to always use the following parameters in the input files for pw.x: wf_collect = .true. diago_full_acc = .true. See documentation on Quantum ESPRESSO for information on these parameters. BEWARE: Sometimes wavefunctions may lose orthogonality during iterative diagonalization. Neither Quantum ESPRESSO nor BerkeleyGW checks for orthogonality of wavefunctions. This may cause erroneous behavior like diverging head of eps0mat and possibly many other things. This problem could be avoided by using SAPO [see 7) above] which keeps wavefunctions orthogonal during iterative diagonalization.

MeanField/ESPRESSO/kgrid.inp

5 5 5 ! numbers of k-points along b1,b2,b3 0.5 0.5 0.5 ! k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step) ! These first two lines are the usual Monkhorst-Pack parameters. 0.0 0.0 0.001 ! a small q-shift (0.0 unshifted, 0.001 shifted by one 1000th of b3) ! This is for WFNq in Epsilon. 0.0 0.5 0.5 ! lattice vectors in Cartesian coordinates (x,y,z) 0.5 0.0 0.5 ! in units of the lattice parameter 0.5 0.5 0.0 ! 2 ! number of atoms in the unit cell 1 -0.125 -0.125 -0.125 ! atomic species and positions in Cartesian coordinates (x,y,z) 1 0.125 0.125 0.125 ! in units of the lattice parameter 0 0 0 ! size of FFT grid .false. ! use time-reversal symmetry. Set to false for BerkeleyGW .false. ! OPTIONAL: k-points in the log file are in Cartesian coordinates .false. ! OPTIONAL: output is in Octopus format # Above: typical values for Si. Below: general description. # nk1 nk2 nk3 ! numbers of k-points in crystal coordinates (b1,b2,b3) # dk1 dk2 dk3 ! k-grid offset (0.0 unshifted, 1.0 shifted by bj/nkj) # dq1 dq2 dq3 ! a small q-shift (0.0 unshifted, 1.0 shifted by bj) # a1x a1y a1z ! lattice vectors in Cartesian coordinates (x,y,z) # a2x a2y a2z ! in arbitrary units (bohr, angstrom, lattice parameter) # a3x a3y a3z ! # n ! number of atoms in the unit cell # s1 x1 y1 z1 ! atomic species and positions in Cartesian coordinates (x,y,z) # ........... ! in the same units as the lattice vectors # sn xn yn zn ! # nr1 nr2 nr3 ! size of FFT grid # trs ! if set to .true., use time-reversal symmetry (do not use this for BerkeleyGW) # Cartesian ! OPTIONAL: set to .true. for k-points in Cartesian coordinates (only in the log file) # octopus ! OPTIONAL: set to .true. to write output file in format suitable for Octopus

MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.html

Input File Description

Program: pw2bgw.x / PWscf / Quantum Espresso

TABLE OF CONTENTS

INTRODUCTION

&INPUT_PW2BGW

prefix | outdir | real_or_complex | symm_type | wfng_flag | wfng_file | wfng_kgrid | wfng_nk1 | wfng_nk2 | wfng_nk3 | wfng_dk1 | wfng_dk2 | wfng_dk3 | wfng_occupation | wfng_nvmin | wfng_nvmax | rhog_flag | rhog_file | rhog_nvmin | rhog_nvmax | vxcg_flag | vxcg_file | vxc0_flag | vxc0_file | vxc_flag | vxc_file | vxc_integral | vxc_diag_nmin | vxc_diag_nmax | vxc_offdiag_nmin | vxc_offdiag_nmax | vxc_zero_rho_core | vscg_flag | vscg_file | vkbg_flag | vkbg_file

INTRODUCTION

Converts the output files produced by pw.x to the input files for BerkeleyGW.

You cannot use USPP, PAW, or spinors in a pw.x run for BerkeleyGW.

You cannot use "K_POINTS gamma" in a pw.x run for BerkeleyGW.
Use "K_POINTS { tpiba | automatic | crystal }" even for the
Gamma-point calculation.

It is recommended to run a pw.x "bands" calculation with "K_POINTS crystal"
and a list of k-points produced by kgrid.x, which is a part of BerkeleyGW
package (see BerkeleyGW documentation for details).

You can also run a pw.x "nscf" calculation instead of "bands", but in this
case pw.x may generate more k-points than provided in the input file of pw.x.
If this is the case for your calculation you will get errors in BerkeleyGW.

Examples showing how to run BerkeleyGW on top of Quantum ESPRESSO including
the input files for pw.x and pw2bgw.x are distributed together with the
BerkeleyGW package.

Structure of the input data:
============================

   &INPUT_PW2BGW
     ...
   /

Namelist: INPUT_PW2BGW

prefix STRING
Status: MANDATORY 
prefix of files saved by program pw.x
outdir STRING
Default: './' 
the scratch directory where the massive data-files are written
real_or_complex INTEGER
Default: 2 
1 | 2
1 for real flavor of BerkeleyGW (for systems with inversion symmetry and
time-reversal symmetry) or 2 for complex flavor of BerkeleyGW (for systems
without inversion symmetry and time-reversal symmetry)
symm_type STRING
Default: 'cubic' 
'cubic' | 'hexagonal'
type of crystal system, 'cubic' for space groups 1 ... 142 and 195 ... 230
and 'hexagonal' for space groups 143 ... 194. Only used if ibrav = 0 in a
pw.x run. Written to BerkeleyGW WFN, RHO, VXC and VKB files but no longer
used (except in SAPO code in BerkeleyGW). You can use the default value for
all systems. Don't set to different values in different files for the same
system or you will get errors in BerkeleyGW.
wfng_flag LOGICAL
Default: .FALSE. 
write wavefunctions in G-space to BerkeleyGW WFN file
wfng_file STRING
Default: 'WFN' 
name of BerkeleyGW WFN output file. Not used if wfng_flag = .FALSE.
wfng_kgrid LOGICAL
Default: .FALSE. 
overwrite k-grid parameters in BerkeleyGW WFN file.
If pw.x input file contains an explicit list of k-points,
the k-grid parameters in the output of pw.x will be set to zero.
Since sigma and absorption in BerkeleyGW both need to know the
k-grid dimensions, we patch these parameters into BerkeleyGW WFN file
wfng_nk1 INTEGER
Default: 0 
number of k-points along b_1 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_nk2 INTEGER
Default: 0 
number of k-points along b_2 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_nk3 INTEGER
Default: 0 
number of k-points along b_3 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_dk1 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_1 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_dk2 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_2 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_dk3 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_3 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_occupation LOGICAL
Default: .FALSE. 
overwrite occupations in BerkeleyGW WFN file
wfng_nvmin INTEGER
Default: 0 
index of the lowest occupied band (normally = 1).
Not used if wfng_occupation = .FALSE.
wfng_nvmax INTEGER
Default: 0 
index of the highest occupied band (normally = number of occupied bands).
Not used if wfng_occupation = .FALSE.
rhog_flag LOGICAL
Default: .FALSE. 
write charge density in G-space to BerkeleyGW RHO file.
Only used for the GPP model in sigma code in BerkeleyGW
rhog_file STRING
Default: 'RHO' 
name of BerkeleyGW RHO output file. Only used for the GPP model in sigma
code in BerkeleyGW. Not used if rhog_flag = .FALSE.
rhog_nvmin INTEGER
Default: 0 
index of the lowest band used for calculation of charge density. This is
needed if one wants to exclude semicore states from charge density used
for the GPP model in sigma code in BerkeleyGW. Make sure to include the
same k-points as in scf calculation. Self-consistent charge density is
used if rhog_nvmin = 0 and rhog_nvmax = 0. Not used if rhog_flag = .FALSE.
BEWARE: this feature is highly experimental and may not work at all in
parallel, with pools, with spins, etc.
rhog_nvmax INTEGER
Default: 0 
index of the highest band used for calculation of charge density. See
description of rhog_nvmin for more details
vxcg_flag LOGICAL
Default: .FALSE. 
write local part of exchange-correlation potential in G-space to
BerkeleyGW VXC file. Only used in sigma code in BerkeleyGW, it is
recommended to use vxc_flag instead
vxcg_file STRING
Default: 'VXC' 
name of BerkeleyGW VXC output file. Only used in sigma code in BerkeleyGW,
it is recommended to use vxc_flag instead. Not used if vxcg_flag = .FALSE.
vxc0_flag LOGICAL
Default: .FALSE. 
write Vxc(G = 0) to text file. Only for testing, not required for BerkeleyGW
vxc0_file STRING
Default: 'vxc0.dat' 
name of output text file for Vxc(G = 0). Only for testing, not required for
BerkeleyGW. Not used if vxc0_flag = .FALSE.
vxc_flag LOGICAL
Default: .FALSE. 
write matrix elements of exchange-correlation potential to text file.
Only used in sigma code in BerkeleyGW
vxc_file STRING
Default: 'vxc.dat' 
name of output text file for Vxc matrix elements. Only used in sigma code
in BerkeleyGW. Not used if vxc_flag = .FALSE.
vxc_integral STRING
Default: 'g' 
'g' | 'r'
'g' to compute matrix elements of exchange-correlation potential in G-space.
'r' to compute matrix elements of the local part of exchange-correlation
potential in R-space. It is recommended to use 'g'. Not used if vxc_flag = .FALSE.
vxc_diag_nmin INTEGER
Default: 0 
minimum band index for diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_diag_nmax INTEGER
Default: 0 
maximum band index for diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_offdiag_nmin INTEGER
Default: 0 
minimum band index for off-diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_offdiag_nmax INTEGER
Default: 0 
maximum band index for off-diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_zero_rho_core LOGICAL
Default: .TRUE. 
set to .TRUE. to zero out NLCC or to .FALSE. to keep NLCC when computing
exchange-correlation potential. This flag has no effect for pseudopotentials
without NLCC. BEWARE: setting vxc_zero_rho_core to .FALSE. will produce
incorrect results. This functionality is only included for testing purposes
and is not meant to be used in a production environment
vscg_flag LOGICAL
Default: .FALSE. 
write local part of self-consistent potential in G-space to
BerkeleyGW VSC file. Only used in SAPO code in BerkeleyGW
vscg_file STRING
Default: 'VSC' 
name of BerkeleyGW VSC output file. Only used in SAPO code in BerkeleyGW.
Not used if vscg_flag = .FALSE.
vkbg_flag LOGICAL
Default: .FALSE. 
write Kleinman-Bylander projectors in G-space to BerkeleyGW VKB file.
Only used in SAPO code in BerkeleyGW
vkbg_file STRING
Default: 'VKB' 
name of BerkeleyGW VKB output file. Only used in SAPO code in BerkeleyGW.
Not used if vkbg_flag = .FALSE.
This file has been created by helpdoc utility.

MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.html

Input File Description

Program: bgw2pw.x / PWscf / Quantum Espresso

TABLE OF CONTENTS

INTRODUCTION

&INPUT_BGW2PW

prefix | outdir | real_or_complex | wfng_flag | wfng_file | wfng_nband | rhog_flag | rhog_file

INTRODUCTION

Converts BerkeleyGW WFN and RHO files to the format of pw.x.
This can be useful, for example, if you generate the plane waves
on top of the valence bands and want to diagonalize them in pw.x.
Look at the documentation for SAPO code in BerkeleyGW for more information.

bgw2pw.x reads common parameters from file prefix.save/data-file.xml and
writes files prefix.save/charge-density.dat (charge density in R-space),
prefix.save/gvectors.dat (G-vectors for charge density and potential),
prefix.save/K$n/eigenval.xml (eigenvalues and occupations for nth k-point),
prefix.save/K$n/evc.dat (wavefunctions in G-space for nth k-point), and
prefix.save/K$n/gkvectors.dat (G-vectors for nth k-point).

bgw2pw.x doesn't modify file prefix.save/data-file.xml so make changes to this
file manually (for example, you will need to change the number of bands if you
are using bgw2pw.x in conjunction with SAPO code in BerkeleyGW).

Structure of the input data:
============================

   &INPUT_BGW2PW
     ...
   /

Namelist: INPUT_BGW2PW

prefix STRING
Status: MANDATORY 
prefix of files saved by program pw.x
outdir STRING
Default: './' 
the scratch directory where the massive data-files are written
real_or_complex INTEGER
Default: 2 
1 | 2
1 for real flavor of BerkeleyGW (for systems with inversion symmetry and
time-reversal symmetry) or 2 for complex flavor of BerkeleyGW (for systems
without inversion symmetry and time-reversal symmetry)
wfng_flag LOGICAL
Default: .FALSE. 
read wavefunctions in G-space from BerkeleyGW WFN file
wfng_file STRING
Default: 'WFN' 
name of BerkeleyGW WFN input file. Not used if wfng_flag = .FALSE.
wfng_nband INTEGER
Default: 0 
number of bands to write (0 = all). Not used if wfng_flag = .FALSE.
rhog_flag LOGICAL
Default: .FALSE. 
read charge density in G-space from BerkeleyGW RHO file
rhog_file STRING
Default: 'RHO' 
name of BerkeleyGW RHO input file. Not used if rhog_flag = .FALSE.
This file has been created by helpdoc utility.

MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.html

Input File Description

Program: pw2bgw.x / PWscf / Quantum Espresso

TABLE OF CONTENTS

INTRODUCTION

&INPUT_PW2BGW

prefix | outdir | real_or_complex | symm_type | wfng_flag | wfng_file | wfng_kgrid | wfng_nk1 | wfng_nk2 | wfng_nk3 | wfng_dk1 | wfng_dk2 | wfng_dk3 | wfng_occupation | wfng_nvmin | wfng_nvmax | rhog_flag | rhog_file | vxcg_flag | vxcg_file | vxc0_flag | vxc0_file | vxc_flag | vxc_file | vxc_integral | vxc_diag_nmin | vxc_diag_nmax | vxc_offdiag_nmin | vxc_offdiag_nmax | vxc_zero_rho_core | vscg_flag | vscg_file | vkbg_flag | vkbg_file

INTRODUCTION

Converts the output files produced by pw.x to the input files for BerkeleyGW.

You cannot use USPP, PAW, or spinors in a pw.x run for BerkeleyGW.

You cannot use "K_POINTS gamma" in a pw.x run for BerkeleyGW.
Use "K_POINTS { tpiba | automatic | crystal }" even for the
Gamma-point calculation.

It is recommended to run a pw.x "bands" calculation with "K_POINTS crystal"
and a list of k-points produced by kgrid.x, which is a part of BerkeleyGW
package (see BerkeleyGW documentation for details).

You can also run a pw.x "nscf" calculation instead of "bands", but in this
case pw.x may generate more k-points than provided in the input file of pw.x.
If this is the case for your calculation you will get errors in BerkeleyGW.

Examples showing how to run BerkeleyGW on top of Quantum ESPRESSO including
the input files for pw.x and pw2bgw.x are distributed together with the
BerkeleyGW package.

Structure of the input data:
============================

   &INPUT_PW2BGW
     ...
   /

Namelist: INPUT_PW2BGW

prefix STRING
Status: MANDATORY 
prefix of files saved by program pw.x
outdir STRING
Default: './' 
the scratch directory where the massive data-files are written
real_or_complex INTEGER
Default: 2 
1 | 2
1 for real flavor of BerkeleyGW (for systems with inversion symmetry and
time-reversal symmetry) or 2 for complex flavor of BerkeleyGW (for systems
without inversion symmetry and time-reversal symmetry)
symm_type STRING
Default: 'cubic' 
'cubic' | 'hexagonal'
type of crystal system, 'cubic' for space groups 1 ... 142 and 195 ... 230
and 'hexagonal' for space groups 143 ... 194. Only used if ibrav = 0 in a
pw.x run. Written to BerkeleyGW WFN, RHO, VXC and VKB files but no longer
used (except in SAPO code in BerkeleyGW). You can use the default value for
all systems. Don't set to different values in different files for the same
system or you will get errors in BerkeleyGW.
wfng_flag LOGICAL
Default: .FALSE. 
write wavefunctions in G-space to BerkeleyGW WFN file
wfng_file STRING
Default: 'WFN' 
name of BerkeleyGW WFN output file. Not used if wfng_flag = .FALSE.
wfng_kgrid LOGICAL
Default: .FALSE. 
overwrite k-grid parameters in BerkeleyGW WFN file.
If pw.x input file contains an explicit list of k-points,
the k-grid parameters in the output of pw.x will be set to zero.
Since sigma and absorption in BerkeleyGW both need to know the
k-grid dimensions, we patch these parameters into BerkeleyGW WFN file
wfng_nk1 INTEGER
Default: 0 
number of k-points along b_1 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_nk2 INTEGER
Default: 0 
number of k-points along b_2 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_nk3 INTEGER
Default: 0 
number of k-points along b_3 reciprocal lattice vector.
Not used if wfng_kgrid = .FALSE.
wfng_dk1 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_1 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_dk2 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_2 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_dk3 REAL
Default: 0.0 
k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step)
along b_3 reciprocal lattice vector. Not used if wfng_kgrid = .FALSE.
wfng_occupation LOGICAL
Default: .FALSE. 
overwrite occupations in BerkeleyGW WFN file
wfng_nvmin INTEGER
Default: 0 
index of the lowest occupied band (normally = 1).
Not used if wfng_occupation = .FALSE.
wfng_nvmax INTEGER
Default: 0 
index of the highest occupied band (normally = number of occupied bands).
Not used if wfng_occupation = .FALSE.
rhog_flag LOGICAL
Default: .FALSE. 
write charge density in G-space to BerkeleyGW RHO file.
Only used for the GPP model in sigma code in BerkeleyGW
rhog_file STRING
Default: 'RHO' 
name of BerkeleyGW RHO output file. Only used for the GPP model in sigma
code in BerkeleyGW. Not used if rhog_flag = .FALSE.
vxcg_flag LOGICAL
Default: .FALSE. 
write local part of exchange-correlation potential in G-space to
BerkeleyGW VXC file. Only used in sigma code in BerkeleyGW, it is
recommended to use vxc_flag instead
vxcg_file STRING
Default: 'VXC' 
name of BerkeleyGW VXC output file. Only used in sigma code in BerkeleyGW,
it is recommended to use vxc_flag instead. Not used if vxcg_flag = .FALSE.
vxc0_flag LOGICAL
Default: .FALSE. 
write Vxc(G = 0) to text file. Only for testing, not required for BerkeleyGW
vxc0_file STRING
Default: 'vxc0.dat' 
name of output text file for Vxc(G = 0). Only for testing, not required for
BerkeleyGW. Not used if vxc0_flag = .FALSE.
vxc_flag LOGICAL
Default: .FALSE. 
write matrix elements of exchange-correlation potential to text file.
Only used in sigma code in BerkeleyGW
vxc_file STRING
Default: 'vxc.dat' 
name of output text file for Vxc matrix elements. Only used in sigma code
in BerkeleyGW. Not used if vxc_flag = .FALSE.
vxc_integral STRING
Default: 'g' 
'g' | 'r'
'g' to compute matrix elements of exchange-correlation potential in G-space.
'r' to compute matrix elements of the local part of exchange-correlation
potential in R-space. It is recommended to use 'g'. Not used if vxc_flag = .FALSE.
vxc_diag_nmin INTEGER
Default: 0 
minimum band index for diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_diag_nmax INTEGER
Default: 0 
maximum band index for diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_offdiag_nmin INTEGER
Default: 0 
minimum band index for off-diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_offdiag_nmax INTEGER
Default: 0 
maximum band index for off-diagonal Vxc matrix elements. Not used if vxc_flag = .FALSE.
vxc_zero_rho_core LOGICAL
Default: .FALSE. 
set to .TRUE. to zero out NLCC or to .FALSE. to keep NLCC when computing
exchange-correlation potential. For details, see Hybertsen & Louie PRB 34,
5390 (1986), Eq. (38) and discussion afterwards
vscg_flag LOGICAL
Default: .FALSE. 
write local part of self-consistent potential in G-space to
BerkeleyGW VSC file. Only used in SAPO code in BerkeleyGW
vscg_file STRING
Default: 'VSC' 
name of BerkeleyGW VSC output file. Only used in SAPO code in BerkeleyGW.
Not used if vscg_flag = .FALSE.
vkbg_flag LOGICAL
Default: .FALSE. 
write Kleinman-Bylander projectors in G-space to BerkeleyGW VKB file.
Only used in SAPO code in BerkeleyGW
vkbg_file STRING
Default: 'VKB' 
name of BerkeleyGW VKB output file. Only used in SAPO code in BerkeleyGW.
Not used if vkbg_flag = .FALSE.
This file has been created by helpdoc utility.

MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.html

Input File Description

Program: bgw2pw.x / PWscf / Quantum Espresso

TABLE OF CONTENTS

INTRODUCTION

&INPUT_BGW2PW

prefix | outdir | real_or_complex | wfng_flag | wfng_file | wfng_nband | rhog_flag | rhog_file

INTRODUCTION

Converts BerkeleyGW WFN and RHO files to the format of pw.x.
This can be useful, for example, if you generate the plane waves
on top of the valence bands and want to diagonalize them in pw.x.
Look at the documentation for SAPO code in BerkeleyGW for more information.

bgw2pw.x reads common parameters from file prefix.save/data-file.xml and
writes files prefix.save/charge-density.dat (charge density in R-space),
prefix.save/gvectors.dat (G-vectors for charge density and potential),
prefix.save/K$n/eigenval.xml (eigenvalues and occupations for nth k-point),
prefix.save/K$n/evc.dat (wavefunctions in G-space for nth k-point), and
prefix.save/K$n/gkvectors.dat (G-vectors for nth k-point).

bgw2pw.x doesn't modify file prefix.save/data-file.xml so make changes to this
file manually (for example, you will need to change the number of bands if you
are using bgw2pw.x in conjunction with SAPO code in BerkeleyGW).

Structure of the input data:
============================

   &INPUT_BGW2PW
     ...
   /

Namelist: INPUT_BGW2PW

prefix STRING
Status: MANDATORY 
prefix of files saved by program pw.x
outdir STRING
Default: './' 
the scratch directory where the massive data-files are written
real_or_complex INTEGER
Default: 2 
1 | 2
1 for real flavor of BerkeleyGW (for systems with inversion symmetry and
time-reversal symmetry) or 2 for complex flavor of BerkeleyGW (for systems
without inversion symmetry and time-reversal symmetry)
wfng_flag LOGICAL
Default: .FALSE. 
read wavefunctions in G-space from BerkeleyGW WFN file
wfng_file STRING
Default: 'WFN' 
name of BerkeleyGW WFN input file. Not used if wfng_flag = .FALSE.
wfng_nband INTEGER
Default: 0 
number of bands to write (0 = all). Not used if wfng_flag = .FALSE.
rhog_flag LOGICAL
Default: .FALSE. 
read charge density in G-space from BerkeleyGW RHO file
rhog_file STRING
Default: 'RHO' 
name of BerkeleyGW RHO input file. Not used if rhog_flag = .FALSE.
This file has been created by helpdoc utility.

MeanField/ESPRESSO/version-4.3.2/pw2bgw.inp

&input_pw2bgw prefix = 'silicon' ! same as in espresso real_or_complex = 1 ! 1 for real or 2 for complex wfng_flag = .true. ! write wavefunction in G-space wfng_file = 'WFN' ! wavefunction file name wfng_kgrid = .false. ! overwrite k-grid in wavefunction file wfng_nk1 = 4 ! ( if espresso input file contains the wfng_nk2 = 4 ! manual list of k-points, the k-grid wfng_nk3 = 4 ! parameters in espresso are set to zero; wfng_dk1 = 0.5 ! since Sigma and absorption both need to know wfng_dk2 = 0.5 ! the k-grid dimensions, we patch these wfng_dk3 = 0.5 ! parameters into the wave-function file ) wfng_occupation = .true. ! overwrite occupations in wavefunction file wfng_nvmin = 1 ! ( set min/max valence band indices; identical to wfng_nvmax = 4 ! scissors operator for LDA-metal/GW-insulator ) rhog_flag = .true. ! write charge density in G-space rhog_file = 'RHO' ! charge density file name vxcg_flag = .true. ! write exchange-correlation potential in G-space vxcg_file = 'VXC' ! exchange-correlation potential file name vxc0_flag = .true. ! write Vxc(G=0) vxc0_file = 'vxc0.dat' ! Vxc(G=0) file name vxc_flag = .false. ! write matrix elements of Vxc vxc_file = 'vxc.dat' ! Vxc matrix elements file name vxc_integral = 'g' ! compute Vxc matrix elements in R- or G-space vxc_diag_nmin = 0 ! min band index for diagonal Vxc matrix elements vxc_diag_nmax = 0 ! max band index for diagonal Vxc matrix elements vxc_offdiag_nmin = 0 ! min band index for off-diagonal Vxc matrix elements vxc_offdiag_nmax = 0 ! max band index for off-diagonal Vxc matrix elements input_dft = 'sla+pz' ! same as in espresso exx_flag = .false. ! set to .true. for hybrids vnlg_flag = .false. ! write Kleinman-Bylander projectors in G-space vnlg_file = 'KBproj' ! Kleinman-Bylander projectors file name vxc_zero_rho_core = .true. ! NLCC: remove core charge when calculating Vxc / # above are typical values for Si. below are the defaults. prefix = 'prefix' real_or_complex = 2 wfng_flag = .false. wfng_file = 'WFN' wfng_kgrid = .false. wfng_nk1 = 0 wfng_nk2 = 0 wfng_nk3 = 0 wfng_dk1 = 0.0 wfng_dk2 = 0.0 wfng_dk3 = 0.0 wfng_occupation = .false. wfng_nvmin = 0 wfng_nvmax = 0 rhog_flag = .false. rhog_file = 'RHO' vxcg_flag = .false. vxcg_file = 'VXC' vxc0_flag = .false. vxc0_file = 'vxc0.dat' vxc_flag = .false. vxc_file = 'vxc.dat' vxc_integral = 'g' vxc_diag_nmin = 0 vxc_diag_nmax = 0 vxc_offdiag_nmin = 0 vxc_offdiag_nmax = 0 input_dft = 'sla+pz' exx_flag = .false. vnlg_flag = .false. vnlg_file = 'VNL' vxc_zero_rho_core = .true.

MeanField/ESPRESSO/version-4.3.2/bgw2pw.inp

&input_bgw2pw prefix = 'silicon' ! same as in espresso real_or_complex = 1 ! 1 for real or 2 for complex wfng_flag = .true. ! read wavefunction in G-space wfng_file = 'WFN' ! wavefunction file name wfng_nband = 0 ! number of bands to write (0 = all) rhog_flag = .true. ! read charge density in G-space rhog_file = 'RHO' ! charge density file name / # above are typical values for Si. below are the defaults. prefix = 'prefix' real_or_complex = 2 wfng_flag = .false. wfng_file = 'WFN' wfng_nband = 0 rhog_flag = .false. rhog_file = 'RHO'

MeanField/ESPRESSO/version-4.3.2/README_patch

This directory contains a patch for espresso-4.3.2 that fixes bugs listed below. Assuming BerkeleyGW is installed in $BGWPATH/BerkeleyGW, to apply the patch execute the following command in the directory containing the espresso-4.3.2 directory: % patch -p0 -i $BGWPATH/BerkeleyGW/MeanField/ESPRESSO/version-4.3.2/espresso-4.3.2-patch espresso-4.3.2 buglist: (1) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> If you run espresso nscf calculation with startingwfc set to file you may get error message saying "cannot read wfc : file not found". This happens because subroutine verify_tmpdir in PW/input.f90 renames data-file.xml to data-file.xml.bck and subroutines read_planewaves and read_wavefunctions in PW/pw_restart.f90 try to read from data-file.xml which doesn't exist. To get around this problem read from .xml.bck in read_planewaves and read_wavefunctions if opening .xml returns error. (2) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Missing "CALL stop_pp ( )" at the end of PP/plan_avg.f90 causes it to crash sometimes. (3) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Sometimes pw.x generates additional k-points in a "nscf" run with an explicit list of k-points. If this is the case for your calculation, there are several ways to go around this problem: * Apply the patch provided with BerkeleyGW. It will prevent pw.x from generating additional k-points if they are provided explicitly, and take care of the normalization of the weights of k-points in a "bands" calculation. * Do not specify the atomic positions in the input file of kgrid.x (set number of atoms = 0). Then pw.x will generate additional k-points which are the correct ones. Also set noinv = .true. in the input file of pw.x if time-reversal symmetry was not used in kgrid.x. * Run a pw.x "bands" calculation instead of "nscf". In this case you have to explicitly specify the occupations in the input file of pw2bgw.x (note that this only works for insulators) and to normalize the weights of k-points to one in the input file of pw.x.

MeanField/ESPRESSO/patch_oldversions/README

This directory contains patches for older versions of espresso that fixes bugs listed below. Assuming BerkeleyGW is installed in $BGWPATH/BerkeleyGW, to apply the patch execute the following command in the directory containing the espresso-xxx directory: % patch -p0 -i $BGWPATH/BerkeleyGW/MeanField/ESPRESSO/patch_oldversions/espresso-xxx-patch espresso buglist: (1) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> If you run espresso nscf calculation with startingwfc set to file you may get error message saying "cannot read wfc : file not found". This happens because subroutine verify_tmpdir in PW/input.f90 renames data-file.xml to data-file.xml.bck and subroutines read_planewaves and read_wavefunctions in PW/pw_restart.f90 try to read from data-file.xml which doesn't exist. To get around this problem read from .xml.bck in read_planewaves and read_wavefunctions if opening .xml returns error. (2) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Missing "CALL stop_pp ( )" at the end of PP/plan_avg.f90 causes it to crash sometimes.

PARATEC

MeanField/PARATEC/README

paratecSGL is available for download through SVN repository at https://civet.berkeley.edu/svn/CODES/paratecSGL/ (only for authorized users). To build with support for BerkeleyGW output, in arch.mk set the line GWWFNPATH to BerkeleyGW/library, and add -DBGW to M4OPTLIBS. Full documentation for PARATEC 5.1.12: https://drive.google.com/open?id=0BxTQVSgElL8nSnZDbEdhRVBoclE Literature: * B. G. Pfrommer, J. Demmel, and H. Simon, "Unconstrained Energy Functionals for Electronic Structure Calculations," J. Comp. Phys. 150, 287 (1999). * B. G. Pfrommer, M. Cote, S. G. Louie, and M. L. Cohen, "Relaxation of Crystals with the Quasi-Newton Method," J. Comp. Phys. 131, 233 (1997). * Mathieu Taillefumier, Delphine Cabaret, Anne-Marie Flank, and Francesco Mauri, "X-ray absorption near-edge structure calculations with pseudopotentials: Application to the K-edge in diamond and alpha-quartz," Phys. Rev. B 66, 195107 (2002). * http://cmsn.drupalgardens.com/sites/cmsn.drupalgardens.com/files/CMSN_Newsletter_Vol2No2.pdf [An older version was available at http://www.nersc.gov/projects/paratec. PARATEC 5.1 produces only the old GW wavefunction format, incompatible with this version of BerkeleyGW. However, you can convert them to the new format using MeanField/Utilities/convert_old_to_new.x.] The pseudopotentials for PARATEC can be generated with the fhi98PP program which is available for download at http://www.fhi-berlin.mpg.de/th/fhi98md/fhi98PP/ 1. Wrapper: PARATEC output for BerkeleyGW is controlled by flags gw_shift, gwc, gwr, gwscreening, gwcscreening, and vxc_matrix_elements. The flags can be combined with an underscore: e.g. output_flags gwr_gwscreening gwr and gwc are incompatible; gwscreening and gwcscreening are incompatible. gw_shift q1 q2 q3 -- generates q-shifted grid, q-vector is in crystal coordinates in units of reciprocal lattice vectors (for WFNq, WFNq_fi) This variable does the same job as the kgrid.x utility. output_flags gwc -- writes complex wavefunctions in G-space, for systems without inversion symmetry about the origin, to file WFN (for all codes). output_flags gwr -- writes real wavefunctions in G-space, for systems with inversion symmetry about the origin, to file WFN (for all codes) output_flags gwscreening -- writes charge density in G-space to file RHO, exchange-correlation potential in G-space to file VXC, and matrix elements of exchange-correlation potential to file vxc.dat (for Sigma). Real if possible and gwc not set, else complex. output_flags gwcscreening -- like gwscreening, except forces complex even if real is possible. vxc_matrix_elements diagmin diagmax offdiagmin offdiagmax -- specifies the range of bands for which to compute diagonal and off-diagonal matrix elements of exchange-correlation potential (for Sigma, in conjunction with output_flags gwscreening) Other key input flags: pw_job {scf, nonselfcon} -- Use scf for initial calculation, nonselfcon for generating BerkeleyGW outputs. (bandstructure does not seem to work) energy_cutoff ecut -- Plane-wave cutoff for wavefunctions, in Ry. number_kpoints -- set to 0 to use k_grid and reduce with symmetries set to -1 to use k_grid and do not reduce with symmetries set to any other number to read from file KPOINTS k_grid nx ny nz -- 3 integers specifying Monkhorst-Pack k-grid dimensions k_grid_shift dx dy dz -- Monkhorst-Pack k-grid shifts (typically 0.0 or 0.5) number_bands nb -- Number of bands to use in calculation. Fraction actually useful or written to BerkeleyGW output determined by next variable. eigspacefrac frac -- Fraction of bands to converge. Setting a higher number_bands and lower eigspacefrac can make the calculation more efficient depending on the diagonalization scheme. 0 < frac <= 1.0. You can find the actual input files for PARATEC and BerkeleyGW in examples/DFT, in PARATEC subdirectories for each example. There are also bgw2para and rho2cd utilities that convert BerkeleyGW files WFN and RHO to PARATEC format. This may be useful, for example, if one generates the plane waves on top of the valence and conduction bands (look into MeanField/SAPO/README for details) and wants to diagonalize them further in PARATEC. There are no input files; bgw2para takes as argument the wfn filename, and it creates files WFN$n.$s and BAND needed for PARATEC. Similarly, rho2cd requires file RHO and it creates file CD. 2. Utilities: -------------------------------------------------------------------------------- PARATEC: K-points -------------------------------------------------------------------------------- TOOL: kptlist.pl Extracts a formatted list of k-points from PARATEC file for use in the Sigma code -------------------------------------------------------------------------------- PARATEC: Q-points -------------------------------------------------------------------------------- TOOL: qptlist.pl Extracts a formatted list of q-points from PARATEC file for use in the Epsilon code

SIESTA

MeanField/SIESTA/README

An example siesta2bgw calculation is provided in examples/DFT/benzene. Please see this example for usage and example siesta and denchar input files. The SIESTA wrapper reads lattice vectors, atomic species and positions from SystemLabel.XV file, k-points from SystemLabel.KP file, eigenvalues from SystemLabel.EIG file, wavefunctions in R-space from SystemLabel{.K$k}.WF$n{.UP|.DOWN}{.REAL|.IMAG}.cube file, symmetry group, kinetic energy cutoffs for wavefunctions and charge density, k-grid dimensions and offsets from the input file, generates reciprocal lattice vectors, rotation matrices, fractional translations, FFT grid and G-vectors, performs FFT from R-space to G-space, and writes the selected range of bands to the output WFN file. Make sure to set up the real space grid in SIESTA/DENCHAR utility same as FFT grid. If the two grids differ the SIESTA wrapper will return an error. The output WFN file can be used as an auxiliary wavefunction for the SAPO code. A full GW/BSE calculation with SIESTA wavefunctions also requires RHO and VXC files. These files can be generated from SystemLabel.RHO{.UP|.DN}.cube, SystemLabel.VT{.UP|.DN}.cube and SystemLabel.VH.cube files obtained with SIESTA/GRID2CUBE utility on SIESTA real space grid. Make sure SIESTA real space grid is equivalent to FFT grid by setting parameter MeshCutoff in SIESTA input file same as kinetic energy cutoff for charge density. Input is read from file siesta2bgw.inp: &input_siesta2bgw systemlabel = 'ammonia' wfng_output_file = 'wfng.lo' rhog_output_file = '' vxcg_output_file = '' ecutwfn = 60.0 ecutrho = 240.0 wfng_nk1 = 1 wfng_nk2 = 1 wfng_nk3 = 1 wfng_dk1 = 0.0 wfng_dk2 = 0.0 wfng_dk3 = 0.0 wfng_ref_flag = .true. wfng_ref_kpoint = 1 wfng_ref_spin = 1 wfng_ref_band = 4 wfng_ref_energy = -5.87 wfng_band_flag = .true. wfng_band_min = 5 wfng_band_max = 28 wfng_energy_flag = .false. wfng_energy_min = 0.0 wfng_energy_max = 0.0 wfng_gamma_real = .true. / Here, lattice vectors, k-points, eigenvalues and wavefunctions in R-space are read from ammonia.XV, ammonia.KP, ammonia.EIG and ammonia.WF$n.cube files, respectively. The kinetic-energy cutoffs for wavefunction and charge density are set to 60 and 240 Ry, respectively. The k-grid is set to the Gamma-point. The SIESTA eigenvalues are shifted in energy so that the HOMO state (1st k-point, 1st spin, 4th band) appears at -5.87 eV. The real parts of resonant SIESTA wavefunctions (from 5th to 28th band) are read from Gaussian Cube files and the imaginary parts are set to zero (wfng_gamma_real), the wavefunctions are brought from R-space to G-space and written to wfng.lo file. The SIESTA charge density and exchange-correlation potential files are not generated.

MeanField/SIESTA/patch/README

This directory contains a patch for denchar-1.4 and grid2cube-1.1.1 in siesta-3.1 that adds support for non-orthogonal cells. The modified versions generate Gaussian Cube files on real-space grid. To apply the patch execute the following command in the directory where you have siesta-3.1: % patch -p0 -i siesta-3.1-patch Use the following keywords in siesta input file: WaveFuncKPointsScale ReciprocalLatticeVectors %block WaveFuncKPoints 0.000 0.000 0.000 %endblock WaveFuncKPoints WriteDenchar T SaveRho T SaveElectrostaticPotential T SaveTotalPotential T MeshCutoff 240.0 Ry Then run denchar for wavefunctions and grid2cube for charge density and potentials. In denchar input file, use keywords LatticeConstant and LatticeVectors same as in siesta input file. Keywords Denchar.{Min|Max}{X|Y|Z} will be ignored. In grid2cube input file, 3rd and 4th lines (shift of the origin of coordinates and nskip) will be ignored. There is also irrbz.py that extracts irreducible wedge from siesta output files prefix.KP and prefix.EIG. This is needed because siesta reduces k-points by time-reversal symmetry only.

MeanField/SIESTA/siesta2bgw.inp

&input_siesta2bgw systemlabel = 'prefix' ! SystemLabel used in SIESTA calculation wfng_output_file = 'wfng.lo' ! file to write generated wavefunctions to rhog_output_file = 'rhog.lo' ! file to write rho(G) (blank = not written) vxcg_output_file = 'vxcg.lo' ! file to write Vxc(G) (blank = not written) ecutwfn = 0.0 ! kinetic energy cutoff (Ry) for wavefunctions ecutrho = 0.0 ! kinetic energy cutoff (Ry) for rho and V wfng_nk1 = 0 ! number of k-points along b1 wfng_nk2 = 0 ! number of k-points along b2 wfng_nk3 = 0 ! number of k-points along b3 wfng_dk1 = 0.0 ! k-grid offset along b1 in units of b1/nk1 wfng_dk2 = 0.0 ! k-grid offset along b2 in units of b2/nk2 wfng_dk3 = 0.0 ! k-grid offset along b3 in units of b3/nk3 wfng_ref_flag = .false. ! shift eigenvalues to match reference state wfng_ref_kpoint = 0 ! reference state k-point index wfng_ref_spin = 0 ! reference state spin index wfng_ref_band = 0 ! reference state band index wfng_ref_energy = 0.0 ! reference state eigenvalue (in eV) wfng_band_flag = .false. ! choose a range of bands (0 = all) wfng_band_min = 0 ! minimum band number wfng_band_max = 0 ! maximum band number wfng_energy_flag = .false. ! choose an energy window wfng_energy_min = 0.0 ! minimum energy (in eV) wfng_energy_max = 0.0 ! maximum energy (in eV) wfng_gamma_real = .false. ! only real wavefunctions at the Gamma point /

Octopus

MeanField/Octopus/README

Octopus is a real-space DFT and TDDFT code available under the GPL from http://www.tddft.org/programs/octopus. Support for BerkeleyGW output is implemented in Octopus since version 4.1.0. For more information, see the Octopus wiki: http://www.tddft.org/programs/octopus/wiki/index.php/BerkeleyGW.

EPM

MeanField/EPM/README

================================================================================ "The empirical pseudopotential method never lost a battle to experiment." -- Marvin Cohen, 2008 ================================================================================ EPM stands for Empirical Pseudopotential Method. It is the plane-wave part of TBPW-1.1 modified to generate input files for BerkeleyGW. Numerous other corrections and improvements have also been made by Georgy Samsonidze and David Strubbe. TBPW-1.1 is available for download from http://www.mcc.uiuc.edu/software/ The input variables are described in epm.inp. Most variables are common to both epm.x and epm2bgw.x, but a few are just for one or the other. The real wavefunctions for systems with inversion symmetry are obtained by applying the Gram-Schmidt process adapted from paratecSGL-1.1.3/src/para/gwreal.f90 To plot silicon band structure calculated with the EPM executable: % epm.x < silicon-epm.in % gnuplot bands.plt Uses variables NumberOfLines, NumberOfDivisions, KPointsAndLabels. To use the explicit form factors and to compute the band gap and the effective masses (mass only correct for Si-like band structures): % epm.x < silicon-epm-ff.in Uses variables gap_flag, gap_file, mass_flag, mass_file. To generate input files for BerkeleyGW executable, use epm2bgw.x. The scripts epm2bgw_cplx.sh and epm2bgw_cplx_spin.sh are just for use with the testsuite. They force complex, or complex and spin-polarized. You can find the actual input files for GW/BSE calculations on top of EPM in directory examples/EPM, as well as testsuite directories Si-EPM, GaAs-EPM, and Si-Wire-EPM. The k-points for the EPM input files can be generated using utility kgrid. Please refer to file MeanField/ESPRESSO/README for details. Virtual crystal approximation (VCA) is implemented within EPM in the form of two pre-processing scripts, ff2vq.py and vca.py. ff2vq.py reads EPM form factors from file form_factors.dat, fits them to the chosen functional form of the V(q) potential, writes potential coefficients to file v_of_q.dat, and writes new form factors computed from V(q) to file vq2ff.dat. This procedure is described by equations (8) and (9) and the accompanying text in Phys. Rev. B 84, 195201 (2011). vca.py reads V(q) potential coefficients from file v_of_q.dat, employs the virtual crystal approximation to compute hybrid form factors, and writes them to file vca_ff.dat. The potential mixing is controlled by identifiers host_material and doping_level hard coded below. This procedure is described by equations (10) -- (12) and the accompanying text in Phys. Rev. B 84, 195201 (2011). The original form factors from file form_factors.dat or the hybrid ones from file vca_ff.dat can be fed to epm.x and epm2bgw.x using keywords LatticeConstant and FormFactors in the input file for epm.x or epm2bgw.x. See example of using these keywords in silicon-epm-ff.in. The README file of TBPW-1.1 follows below. ================================================================================ TBPW-1.1 ======================================== Author/Affiliation -------------------- * Dyutiman Das, UIUC * William Mattson, UIUC * Nichols A. Romero, UIUC * Richard M. Martin, UIUC ======================================== Author email -------------------- nromero@uiuc.edu ======================================== Description of Software -------------------- TBPW is an electronic structure code primarily intended for pedagogical purposes. It is written from the ground-up in a modular style using Fortran 90. This code is composed of two distinct parts: a tightbinding (TB) and plane wave (PW). Additionally, there is a plane wave density (PWD) code which outputs the electron density on a grid. The main characteristics of these codes are: * Readily provides band structure plots * TB implemented using a rotation matrix formalism allows the use of orbitals with arbitrary angular momentum l * PW implemented using the option of diagonalisation via direct-inversion Send email to tbpw-subscribe@mcc.uiuc.edu to subscribe to the mailing list, tbpw@mcc.uiuc.edu This material is based upon work supported by the NSF under Award No. 99-76550 and the DOE under Award No. DEFG-96-ER45439 ======================================== Submitted -------------------- 2003-01-31 ======================================== Disclaimer -------------------- Developed by Electronic Structure Group, University of Illinois, Department of Physics, http://www.physics.uiuc.edu/research/ElectronicStructure/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. * Neither the names of the Electronic Structure Group, the University of Illinois, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. ======================================== Copyright -------------------- University of Illinois Open Source License. Copyright (c) 2003, University of Illinois Board of Trustees. All rights reserved. Users also agree to terms of License Agreement available at http://www.mcc.uiuc.edu/ ================================================================================

MeanField/EPM/epm.inp

# BEWARE: you cannot comment out tags with # in EPM! # any occurrence of a tag will be found and read. # These parameters are only for epm2bgw real_or_complex 1 # 1 = real, 2 = complex. default is complex. wfng_flag T # Write wavefunction file (default F) wfng_file WFN # filename (default WFN) KPointNumbers 5 5 5 # number of points in k-grid in each direction b1,b2,b3 KPointOffsets 0.5 0.5 0.5 # shift in k-grid in each direction b1,b2,b3 rhog_flag T # Write density file (default F) rhog_file RHO # filename (default RHO) vxcg_flag T # Write xc potential file (default F) vxcg_file VXC # filename (default VXC) vxc_flag T # Write VXC matrix element file (default F) vxc_file vxc.dat # filename (default vxc.dat) vxc_diag_nmin 1 # minimum band to write diagonal matrix elements (default 0) vxc_diag_nmax 8 # maximum band to write diagonal matrix elements (default 0) vxc_offdiag_nmin 1 # minimum band to write off-diagonal matrix elements (default 0) vxc_offdiag_nmax 8 # maximum band to write off-diagonal matrix elements (default 0) disable_symmetries F # set to true to write no symmetries (default F) # EPM does not really do a spin-polarized calculation, but can write two copies of everything nspin 1 # set to 2 to write spin up and spin down (default 1) temperature 0 # kT in eV for Fermi-Dirac distribution occupations (only for BerkeleyGW output) # The Fermi level is taken as the mid-gap. FFTGrid 16 16 16 # FFT grid for computing density (default: determined from EnergyCutoff) # These parameters are common to epm and epm2bgw # Set form factor parameters (see examples in form_factors.dat), # or default is to use V(q) from atomPotentialMod (only for H,Si,Ga,As) FormFactors 5.43 -0.224 0.055 0.072 0.000 0.000 0.000 # 0 is for LAPACK direct diagonalization (default), 1 for conjugate gradients DiagonalizationSwitch 0 AbsoluteTolerance -1.0d0 # tolerance for LAPACK diagonalization (default -1 means machine precision) CGIterationPeriod 5 # parameter for conjugate gradients (default 3) CGTolerance 1.0d-10 # parameter for conjugate gradients (1d-5) InputEnergiesInEV # Rydberg is default EnergyCutoff 11.0 # plane-wave cutoff for the potential (and wavefunctions) NumberOfDimensions 3 # dimensionality of the system (default 3) #LatticeConstantFormat Angstrom # default is Bohr LatticeConstant 10.2612 # in units given above LatticeVectors # in lattice constant units 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 NumberOfAtoms 2 NumberOfSpecies 1 ChemicalSpeciesLabel # index, atomic number, name 1 14 Si AtomicCoordinatesFormat ScaledByLatticeVectors # ScaledByLatticeVectors (default) is in crystal coordinates # ScaledCartesian is in units of LatticeConstant AtomicCoordinatesAndAtomicSpecies # x, y, z, species index -0.125 -0.125 -0.125 1 0.125 0.125 0.125 1 NumberOfBands 8 NumberOfOccupiedBands 4 # note: you cannot really do metals, occupations are fixed. KPointsScale ReciprocalLatticeVectors # default; other choice is TwoPi/a KPointsList 19 # number of k-points supplied 0.100000000 0.100000000 0.100000000 2.0 # kx, ky, kz, weight (will be renormalized) 0.100000000 0.100000000 0.300000000 6.0 0.100000000 0.100000000 0.500000000 6.0 0.100000000 0.100000000 0.700000000 6.0 0.100000000 0.100000000 0.900000000 6.0 0.100000000 0.300000000 0.300000000 6.0 0.100000000 0.300000000 0.500000000 12.0 0.100000000 0.300000000 0.700000000 12.0 0.100000000 0.300000000 0.900000000 12.0 0.100000000 0.500000000 0.500000000 6.0 0.100000000 0.500000000 0.700000000 12.0 0.100000000 0.500000000 0.900000000 6.0 0.100000000 0.700000000 0.700000000 6.0 0.300000000 0.300000000 0.300000000 2.0 0.300000000 0.300000000 0.500000000 6.0 0.300000000 0.300000000 0.700000000 6.0 0.300000000 0.500000000 0.500000000 6.0 0.300000000 0.500000000 0.700000000 6.0 0.500000000 0.500000000 0.500000000 1.0 # for plotting band structures; used if KPointsList not present NumberOfLines 4 NumberOfDivisions 20 KPointsScale ReciprocalLatticeVectors # same as above KPointsAndLabels 0.500 0.500 0.500 L 0.000 0.000 0.000 G 0.500 0.000 0.500 X 0.625 0.250 0.625 U 0.000 0.000 0.000 G # These parameters are only for epm. Find band gap and effective mass. gap_flag F # default F gap_file bandgap.dat # filename (default gap.dat) # Note: effective mass only works for silicon-like band structures. mass_flag F # default F mass_file effmass.dat # filename (default mass_file)

ICM

MeanField/ICM/README

This program reads the wavefunction file in Gaussian Cube or XCrySDen XSF format and computes the Coulomb integral within an image charge model. It is based on Visual/surface.cpp code, so the input parameter file formats for the two codes are quite similar. You can find more details in Visual/surface.inp and Visual/README. Input is read from file icm.inp: inputfilename C6H6.b_15.cube inputfileformat cube threshold 0.99 threshold_power 1 coulomb_power 1 mirrorplaneorigin 0.0 0.0 -2.0 mirrorplanenormal 0.0 0.0 1.0 mirrorplaneunit angstrom uc F uco 0.0 0.0 0.0 ucv 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 ucu latvec sc T sco -0.5 -0.5 -0.5 scv 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 scu latvec In the above example, the HOMO wavefunction of benzene is read from Gaussian Cube file. The wavefunction is placed in the center of the supercell (see the meaning of uc, uco, ucv, ucu, sc, sco, scv, scu parameters in Visual/surface.cpp). The parts of the wavefunction outside an isosurface that contains 99% of the charge density are dropped (parameters threshold and threshold_power have the same meaning as isovalue and power in Visual/surface.cpp). Parameter coulomb_power tells the code whether the wavefunction in the Coulomb integral needs to be squared. Set both powers to 1 if the wavefunction file contains the squared amplitude as produced by ESPRESSO, and to 2 for the linear amplitude as in PARATEC or SIESTA. The mirror plane is defined by parameters mirrorplaneorigin and mirrorplanenormal, in the above example it is parallel to the xy plane crossing the z axis at -2 Angstrom. Problems may occur with non-orthogonal unit cells; use of cubic cells is recommended.

Utilities

MeanField/Utilities/README

================================================================================ MeanField utilities ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004) -------------------------------------------------------------------------------- degeneracy_check.x: Determine which numbers of bands do not break a degenerate subspace, to avoid warnings or errors in Epsilon, Sigma, and BSE codes. Supply any number of binary WFN files as command- line arguments, and a list of numbers that are acceptable for all k-points in all files will be written to standard output. mf_convert_wrapper.sh: Converts WFN/RHO/VXC files between binary and ASCII. This can be useful for moving files correctly between big- and little-endian machines, or for examining the contents of a file (though wfn_rho_vxc_info.x is more user-friendly). Using this wrapper script, the flavor (real/complex), type of file, and binary/ASCII is determined automatically. wfn_rho_vxc_info.x: Prints the contents of the header of a (binary) WFN, RHO, or VXC file in a clearly labeled format, for human inspection. wfnmerge.x: Merges many WFN files into one. It assumes that all input files have the same number and same ordering of G-vectors for the charge density. The number and name of input files is read from "wfnmerge.inp", as well is the kgrid and the kshift. FAQ: Q: Why would someone want to use this? A: For example, maybe to do a converged calculation one needs to include a large number of unoccupied states. There may not be the resources (either CPUs or wallclock) to do this all in one shot, so it may be beneficial to split up a calculation of kpoints (e.g., 4x4x4 MP grid) into smaller pieces and then add up the final wavefunctions. Q: What is the deal with kpoint weights? A: Quantum Espresso renormalizes the kpoint weights that you use in a calculation. If you are splitting up a MP grid into different groups of kpoints, and each group is normalized, the relative weights between kpoints in different groups is no longer correct. BerkeleyGW does not make use of the kpoint weights (except for in determining whether the Fermi level is reasonable for metallic calculations). So for most uses the fact that these weights are incorrect does not matter. If it matters to you, you can simply modify wfnmerge to read in the kpoint weights of your choosing. scissors2eqpx: Write an eqp.dat file based on a WFN file and scissors parameters. For testing equivalence of eqp_corrections and scissors. fix_occ.x: Fix the occupations of a WFN file. This is useful if you have split a large nscf calculations into smaller blocks, and you want the occupations of the merged WFN to be consistent. It can also fix inconsistencies in the occupations and in the Fermi energy for metals. wfn_dotproduct.x Form the overlap between the bands in two wavefunction files. If they are copies of the same file, you can check orthonormality. Only bands at corresponding k-points are considered, since the overlap is zero by Bloch`s theorem if the k-points differ. Warning: a known issue is possible errors from gmap when relating k-points by symmetry operations. wfn_time_reversal.x Give a WFN file with a k-grid reduced by time-reversal symmetry, and get a new WFN file with the k-points unfolded by time-reversal symmetry. This can save up to half the time in the non-self-consistent DFT calculations for input to BerkeleyGW. It can be used after calculating k-points from kgrid.x with time-reversal symmetry, or from 'automatic' k-points from Quantum ESPRESSO. Either use VXC, or add the new k-points to vxc.dat by hand according to the rule = *.

MeanField/Utilities/wfnmerge.inp

WFN.OUT ! name of output WFN file 4 4 4 ! final k-grid 0.0 0.0 0.0 ! final k-shift 2 ! total number of input WFN files 8 ! total number of k-points in all input WFN files wfn_0/WFN ! name of 1st input WFN file wfn_1/WFN ! name of 2nd input WFN file 1.0 ! relative weight of 1st input WFN file 1.0 ! relative weight of 2nd input WFN file

MeanField/Utilities/fix_occ.inp

WFN_in ! input WFN WFN_out ! output WFN 0 ! original number of electrons in WFN_in (0 to autodetect) 0 ! extra charge to put in

SAPO

MeanField/SAPO/README

The SAPO (Simple Approximate Physical Orbitals) code reads DFT wavefunctions from WFN file, generates additional wavefunctions on top of them, and writes both to another WFN file. It can generate plane waves, decompose them into irreducible representations of the space group of the Bravais lattice or the crystal, and orthonormalize them with respect to DFT wavefunctions. It can insert SIESTA wavefunctions read from auxiliary WFN file in between plane waves and orthonormalize them altogether. It can apply a random variation to the plane waves and SIESTA wavefunctions or generate completely random wavefunctions and orthonormalize them. It can correct eigenvalues during orthonormalization or perform subspace diagonalization. It can drop the plane waves and SIESTA wavefunctions which have a large overlap with DFT wavefunctions. It can keep wavefunctions with the eigenvalues in a given energy range. It can extract eigenvalues and plane wave coefficients from WFN file for plotting purposes. The SAPO method is described in Phys. Rev. Lett. 107, 186404 (2011) 2012-12-24 (gsm): added iterative Davidson diagonalization, see examples/DFT/Si2_sapo for details Note: When using iterative Davidson diagonalization, it is recommended to generate VXC rather than vxc.dat in pw2bgw run, then compute matrix elements of VXC between SAPO wavefunctions. This is more consistent than using vxc.dat because vxc.dat is computed between ESPRESSO wavefunctions, and those might be slightly different from SAPO wavefunctions. Note: wfng_input_file should contain all occupied orbitals (and may or may not contain some unoccupied orbitals), otherwise occupations written to wfng_output_file will be wrong. Note: Symmetrization of planewaves (sapo_symmetry .gt. 0) has no effect on a SAPO calculation since it is just a linear combination in a degenerate subspace. It is currently disabled because it requires symmetry subroutines from Quantum ESPRESSO which are not compatible with our BSD-type license. To enable it: open MeanField/SAPO/pw.f90; comment out 'die'; uncomment calls to 's_axis_to_cart', 'find_group', 'set_irr_rap', and 'divide_class'; and link the corresponding routines from Quantum ESPRESSO. Input is read from file sapo.inp: &input_sapo wfng_input_file = 'wfng.in' wfng_aux_file = '' vlr_input_file = '' vnlg_input_file = '' wfng_output_file = 'wfng.out' sapo_band_number = 0 sapo_planewave_min = 1 sapo_planewave_max = 580 sapo_energy_shift = 0.0 sapo_energy_match = .true. sapo_symmetry = 2 sapo_print_ir = .true. aux_flag = .false. aux_band_min = 0 aux_band_max = 0 aux_energy_shift = 0.0 sapo_random = 1 sapo_random_ampl = 1.0d-3 sapo_overlap_flag = .false. sapo_overlap_max = 0.0 sapo_orthonormal = .true. sapo_ortho_block = 0 sapo_ortho_order = 0 sapo_ortho_energy = .false. sapo_energy_sort = .false. sapo_hamiltonian = .false. sapo_energy_range = .false. sapo_energy_min = 0.0 sapo_energy_max = 0.0 sapo_check_norm = .false. sapo_plot_kpoint = 0 sapo_plot_spin = 0 sapo_plot_bandmin = 0 sapo_plot_bandmax = 0 sapo_plot_pwmin = 0 sapo_plot_pwmax = 0 sapo_eigenvalue = .false. sapo_projection = 0 sapo_amplitude = .false. sapo_ampl_num = 0 sapo_ampl_del = 0.0 sapo_ampl_brd = 0.0 / Here, the wavefunctions are read from wfng.in file and written to wfng.out file. The parameter sapo_band_number specifies the number of wavefunctions to be read from the input file (if set to 0 all the wavefunctions will be read). The PW wavefunctions will be constructed from plane waves ranging from 1 (sapo_planewave_min) to 580 (sapo_planewave_max). The kinetic energies of the plane waves will be shifted to match the eigenvalues of the input wavefunctions (sapo_energy_match). The plane waves will be decomposed into irreducible representations of the space group of the Bravais lattice (sapo_symmetry = 2), and the decomposition will be printed to the standard output (sapo_print_ir). The auxiliary wavefunctions will not be inserted in between the PW wavefunctions (aux_flag). A random variation (sapo_random = 1) with a small amplitude (sapo_random_ampl = 1.0d-3) will be added to the PW wavefunctions. The PW wavefunctions will be orthonormalized with respect to the valence and conduction bands (sapo_orthonormal) in the ascending order with respect to energy (sapo_ortho_order = 0). The orthonormality check will not be performed (sapo_check_norm). The energy eigenvalues, the projections of wavefunctions onto plane waves, and the squared absolute values of amplitudes of the wavefunctions with respect to kinetic energies of plane waves will not be plotted (sapo_eigenvalue, sapo_projection, and sapo_amplitude). The auxiliary wavefunctions can be used in two different ways: (1) Use hybrid valence wavefunctions as wfng_input_file and LDA conduction wavefunctions as wfng_aux_file, set sapo_planewave_min and sapo_planewave_max to 0, sapo_orthonormal to .true. and sapo_ortho_block to 1. This way you will get a good starting point for nscf hybrid calculations in PARATEC or ESPRESSO. (2) Use Siesta wrapper in MeanField/SIESTA directory to construct the resonant states from SIESTA wavefunctions (look into MeanField/SIESTA/README for details on how to use siesta2bgw), feed them to the SAPO code through wfng_aux_file parameter, and generate continuum states from plane waves by setting sapo_planewave_max to a large number. Also set sapo_orthonormal, sapo_ortho_block and sapo_ortho_order to orthonormalize the resonant and continuum states in the desired order with respect to the bound states from PARATEC or ESPRESSO. You may want to set sapo_ortho_energy to .true. for correcting the eigenvalues during the orthonormalization, or to set sapo_hamiltonian to .true. for correcting both the wavefunctions and the eigenvalues by diagonalizing the Hamiltonian. The latter requires the local potential file in Gaussian Cube format (vlr_input_file), and optionally the non-local pseudopotential file (vnlg_input_file). Finally, set sapo_energy_sort to .true. for sorting the resonant and continuum states by their eigenvalues before writing them to the output file. You may also set sapo_energy_range to .true. for keeping the eigenvalues in the energy range of sapo_energy_min to sapo_energy_max. PS: If you don't know or don't want to manually set sapo_planewave_min and aux_band_min, set both of them to 1, sapo_overlap_flag to .true., and sapo_overlap_max to 0.3. This will automatically throw away plane-waves and auxiliary states that have large overlaps (scalar products > 0.3) with DFT states and among themselves. The scalar products of PW and AUX states with DFT states will be written to files overlap_dft_k#_s#.dat, and the scalar products of PW states with AUX states will be written to files overlap_aux_k#_s#.dat, so you can inspect what states were thrown away after the run. This useful feature is informally known as boverlap, in honor of Brad Malone who first proposed this idea. This confirms once again that evolution is a byproduct of laziness.

MeanField/SAPO/sapo.inp

&input_sapo wfng_input_file = 'wfng.pw' ! file to read DFT wavefunctions from wfng_aux_file = 'wfng.lo' ! file to read auxiliary wavefunctions from vscg_input_file = 'vscg' ! file to read self-consistent potential ! in G-space for constructing Hamiltonian ! (generated by pw2bgw.x from Quantum ESPRESSO) vkbg_input_file = 'vkbg' ! file to read Kleinman-Bylander projectors ! in G-space for constructing Hamiltonian ! (generated by pw2bgw.x from Quantum ESPRESSO) wfng_output_file = 'wfng' ! file to write generated wavefunctions to sapo_band_number = -1 ! number of DFT wavefunctions to use ! (set to -1 to use all wavefunctions found ! in wfng_input_file) sapo_planewave_min = 0 ! indices of the lowest and highest plane waves sapo_planewave_max = 0 ! to construct wavefunctions from (0 = none) sapo_energy_shift = 0.0 ! energy shift for PW kinetic energies (eV) sapo_energy_match = .false. ! match PW kinetic energies & DFT eigenvalues sapo_symmetry = 0 ! 0 = none, 1 = crystal, 2 = lattice symmetry sapo_print_ir = .false. ! print irreducible representations of PW aux_flag = .false. ! insert auxiliary wavefunctions in between PW aux_band_min = 0 ! minimum and maximum band indices of auxiliary aux_band_max = 0 ! wavefunctions (0 = all) aux_energy_shift = 0.0 ! energy shift for auxiliary eigenvalues (eV) sapo_random = 0 ! 0 = none, 1 = small variation, 2 = random sapo_random_ampl = 0.0 ! amplitude of the random variation sapo_random_norm = .false. ! normalize randomized wavefunctions sapo_overlap_flag = .false. ! drop PW & AUX states that have a large ! overlap with DFT states sapo_overlap_max = 0.0 ! maximum scalar product of PW & AUX with DFT sapo_orthonormal = .false. ! orthonormalize PW & AUX wavefunctions wrt DFT sapo_ortho_block = 0 ! 0 = PW/AUX, 1 = AUX/PW, 2 = ordered in energy sapo_ortho_order = 0 ! 0 = ascending, 1 = descending order in energy sapo_ortho_energy = .false. ! correct PW & AUX eigenvalues by perturbative ! approach during orthonormalization sapo_energy_sort = .false. ! sort PW & AUX eigenvalues in ascending order sapo_hamiltonian = .false. ! correct PW & AUX wavefunctions & eigenvalues ! by diagonalizing subspace Hamiltonian or ! by iteratively diagonalizing Hamiltonian sapo_ham_nrestart = 0 ! maximum number of iterative diagonalization ! restarts with random initial wavefunctions ! for k-points/spins that didn`t converge sapo_ham_ndiag = 0 ! maximum number of subspace diagonalization ! steps during iterative diagonalization sapo_ham_ndim = 0 ! maximum number of basis functions in units ! of the total number of wavefunctions, ! same as diago_david_ndim in pw.x sapo_ham_tol = 0.0 ! tolerance on the maximum norm of residual ! vectors for iterative diagonalization (Ry) sapo_ham_resinc = .false. ! stop expanding the basis set and update ! the wavefunctions when the maximum norm ! of residual vectors starts increasing sapo_do_all_bands = .false. ! orthonormalize and diagonalize DFT & PW & AUX ! wavefunctions or PW & AUX wavefunctions sapo_energy_range = .false. ! keep PW & AUX eigenvalues in the energy range sapo_energy_min = 0.0 ! minimum energy for PW & AUX eigenvalues (Ry) sapo_energy_max = 0.0 ! maximum energy for PW & AUX eigenvalues (Ry) sapo_check_norm = .false. ! check orthonormality of wavefunctions sapo_plot_kpoint = 0 ! k-point index (0 = all) for output plots sapo_plot_spin = 0 ! spin index (0 = all) for output plots sapo_plot_bandmin = 0 ! range of band indices (0 = all) for output sapo_plot_bandmax = 0 ! eigenvalue, projection and amplitude plots sapo_plot_pwmin = 0 ! range of plane wave indices (0 = all) for sapo_plot_pwmax = 0 ! output projection plots sapo_eigenvalue = .false. ! plot energy eigenvalues wrt band index (eV) sapo_projection = 0 ! plot projections of wavefunctions onto PW ! 0 = none, 1 = wrt band, 2 = wrt PW, 4 = both sapo_amplitude = .false. ! plot squared absolute values of amplitudes of ! wavefunctions wrt kinetic energies of PW (Ry) sapo_ampl_num = 0 ! number of points on the kinetic energy scale sapo_ampl_del = 0.0 ! separation between the adjacent points (Ry) sapo_ampl_brd = 0.0 ! broadening for wavefunction amplitudes (Ry) /

Epsilon

Epsilon/README

================================================================================ GW code: Epsilon ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (September, 2011) Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 S. Ismail-Beigi (2002) Version 0.1 G. M. Rignanese, E. Chang, X. Blase (1998) Version 0.0 M. Hybertsen (1985) ------------------------------------------------------------------------------- Description: Epsilon is the name of the code that generates the polarizability matrix and the inverse dielectric matrix for a bulk or nanoscale system. The main result of the Epsilon code is the generation of epsmat which can be used in a Sigma or BSE calculation. ------------------------------------------------------------------------------- Required Input: epsilon.inp Input parameters. See example in this directory. WFN This is linked to the unshifted grid. WFNq This is linked to the shifted grid. When a shift is not required, this can be the same file as WFN (i.e. for semiconductor or graphene screening with spherical or box truncation). Auxiliary Files: (output files from previous runs, used as input to speed up calculation) chimat(.h5) Polarizability matrix. No need to recalculate matrix elements. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). chi0mat(.h5) Polarizability matrix at q=0. No need to recalculate matrix elements. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). The files below are used if eqp_corrections is set in epsilon.inp. The corrected eigenvalues are used for constructing the polarizability matrix. eqp.dat A list of quasiparticle energy corrections for the bands in WFN. eqp_q.dat A list of quasiparticle energy corrections for the bands in WFNq. ------------------------------------------------------------------------------- epsilon.inp Please see example epsilon.inp in this directory for more complete options. ------------------------------------------------------------------------------- Output Files: espmat(.h5) Inverse dielectric matrix (q<>0). The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). eps0mat(.h5) Inverse dielectric matrix (q->0). The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). epsilon.log The log file containing values of chimat and epsmat. chi_converge.dat Convergence chi with respect to empty orbitals. Columns: number of conduction bands, Re chi(G=0,G'=0,q), extrapolated Re chi(G=0,G'=0,q), Re chi(G=Max,G'=Max,q), extrapolated Re chi(G=Max,G'=Max,q) ------------------------------------------------------------------------------- Tricks and hints: 1. Comments on convergence of epsilon_cutoff There are many ways to check convergence of this parameter: -Ideally, the inverse epsilon matrix is almost diagonal for large G vectors. So, for small ( G , G' ) it is usually large but, for G or G' close to G_max, it is smaller by a factor of 100, more or less. Check if the ratio between the greatest and lowest matrix elements is large. -Alternatively, one can check if epsinv( G_max , G'_max ) is close to 1 for G = G'. It should be about 0.999 or so. Note that 0.9 isn't "close to 1" in this case! Also check if epsinv( G_max , G'_max ) is indeed small for G != G'. 2. Comments on the null point The null point (Gamma point) is treated in a special manner. In input, declare it as slightly shifted from the true Gamma point: 0.0000 0.0050 0.0050 1.0 1 This is the only k-point with itestq=1 instead of 0! The magnitude of this vector must be small: of order 0.01 or smaller for less than 100 points in full Brillouin zone. If the density of points in BZ increases, that magnitude should decrease accordingly. 3. Macroscopic dielectric constant In GW, the screened interaction gives the formula: eps(G,G';q) = delta_GG' - [4pi e^2/(q+G)^2 ] chi(G,G';q) where chi(G,G';q) is the polarizability (P in the literature). if G=0 and q=0 then we let eps(0,G';q) = delta_0G' - lim(q->0) [4pi/(q)^2] chi(0,G';q) always check chi(0,0;q->0) and eps^(-1)(0,0;q->0) in epsilon.log 1/eps^(-1)(0,0;q->) should be the macroscopic epsilon, local-field effects 1/(1-4*pi*chi(0,0;q->0)*V_c(0) should also be (roughly) the macroscopic epsilon, without local-field effects 4. Merging epsmat files The Epsilon code is complicated and involves lots of computation. Frequently, it is useful to calculate the epsilon matrix for a small number of q-points, and later put all those pieces of matrix into a big epsmat file. Use epsmat_merge to do this. See below. Notes: -epsilon cutoff *must* be the same for all files to be merged -The ordering of q-points in the input file must correspond to the ordering of epsmat files: the first file has the first set of points, the second file has the second and so on. 5. Utilities: ------------------------------------------------------------------------------- Epsilon: binary/ASCII conversion ------------------------------------------------------------------------------- TOOLS: epsbinasc, epsascbin USAGE: simply type name of executable. The input file is named epsconv.inp. ------------------------------------------------------------------------------- -------- WFN/RHO/VXC binary/ASCII conversion ------------------------ ------------------------------------------------------------------------------- TOOL: mf_convert_wrapper.sh USAGE: ./mf_convert_wrapper.sh infile outfile Real/complex, bin/asc, file type, is automatically detected. ------------------------------------------------------------------------------- Epsilon: merging ------------------------------------------------------------------------------- TOOL: epsmat_merge USAGE: epsmat_merge.[real/cplx].x Merges the content of multiple binary epsmat files into an output file called 'epsmat', concatenating data. See input file epsmat_merge.inp, for specification of cutoff, q-points, and input epsmat filenames.

Epsilon/epsilon.inp

# epsilon.inp # Energy cutoff for the dielectric matrix, in Ry. The dielectric matrix # $\varepsilon_{GG'}$ will contain all G-vectors with kinetic energy $|q+G|^2$ # up to this cutoff. #[unit=Ry] epsilon_cutoff 35.0 # Total number of bands (valence+conduction) to sum over. Defaults to the # number of bands in the WFN file minus 1. #number_bands 1000 # Specify the Fermi level (in eV), if you want implicit doping # Note that value refers to energies AFTER scissor shift or eqp corrections. #fermi_level 0.0 # The Fermi level is treated as an absolute value # or relative to that found from the mean field (default) # # #fermi_level_absolute #fermi_level_relative # RECOMMENDED fast FFTW truncation schemes # The Coulomb Interaction is cutoff on the edges of # the Wigner-Seitz Cell in the non-periodic directions # Periodic directions are a1, a2 for slabs and a3 for wires # # #cell_box_truncation #cell_wire_truncation #cell_slab_truncation # Analytic, but non-Wigner-Seitz Cell Truncation #spherical_truncation # For Spherical Truncation, radius in Bohr #coulomb_truncation_radius 10.00 # Frequency dependence of the inverse dielectric matrix. # Set to 0 to compute the static inverse dielectric matrix (default). # Set to 2 to compute the full frequency dependent inverse dielectric matrix. # Set to 3 to compute the two frequencies needed for Godby-Needs GPP model. #frequency_dependence 0 # Plasma frequency (eV) needed for Contour-Deformation method. The exact value # is unimportant, especially if you have enough imaginary frequency points. We # recommend you keep this value fixed at 2 Ry. #plasma_freq 27.21138506d0 # For frequency_dependence 3, the value of the purely imaginary frequency, in eV: #imaginary_frequency 27.21138506d0 # ### Parameters for full-frequency-dependent calculations, in eV. # Three methods are available, depending on the value of [[frequency_dependence_method]]: # # - 0 - Real-Axis formalism with Adler-Wiser formula: # - A uniform frequency grid is set up from [[init_frequency]] (defaults to 0), # up to [[low_frequency_cutoff]], with a spacing of [[delta_frequency]] between # two frequencies. # - A non-uniform frequency grid is setup from [[low_frequency_cutoff]] to # [[high_frequency_cutoff]], where the frequency spacing gets increased by # [[delta_frequency_step]]. # # - 1 - Real-Axis formalism with spectral method: # - A uniform frequency grid is set up from [[init_frequency]] (defaults to 0), # up to [[low_frequency_cutoff]], with a spacing of [[delta_frequency]] between # two frequencies. # - A non-uniform frequency grid is setup from [[low_frequency_cutoff]] to # [[high_frequency_cutoff]], where the frequency spacing gets increased by # [[delta_frequency_step]]. # - A separate frequency grid is set-up for the spectral function. The variables # [[init_sfrequency]], [[delta_sfrequency]], [[delta_sfrequency_step]], # [[sfrequency_low_cutoff]], and [[sfrequency_high_cutoff]] define this grid, in # an analogy to the flags used to define the grid for the polarizability matrix. # # - 2 - Contour-Deformation formalism with Adler-Wiser formula (**default**). # - A uniform frequency grid is set up from [[init_frequency]] (defaults to 0), # up to [[low_frequency_cutoff]], with a spacing of [[delta_frequency]] between # two frequencies. # - A frequency grid with [[number_imaginary_freqs]] is set-up on the imag axis. # # # Full frequency dependence method for the polarizability, if [[frequency_dependence]]==2: # # - 0: Real-Axis formalism, Adler-Wiser formula. # - 1: Real-Axis formalism, spectral method (PRB 74, 035101, (2006)) # - 2: Contour-Deformation formalism, Adler-Wiser formula. #frequency_dependence_method 2 # # # Broadening parameter for each val->cond transition. # It should correspond to the energy resolution due to k-point sampling, # or a number as small as possible if you have a molecule. # The default value is 0.1 for method 0 and 1, and 0.25 for method 2. #broadening 0.1 # # Lower bound for the linear frequency grid. #init_frequency 0.0 # # Upper bound for the linear frequency grid. # For methods 0 and 1, it is also the lower bound for the non-uniform frequency grid. # Should be larger than the maximum transition, i.e., the # energy difference between the highest conduction band and the lowest valence band. # The default is 200 eV for method 0 and 1, and 10 eV for method 2. # For method 2, you can increase frequency_low_cutoff if you wish to use # the Sigma code and look into QP states deep in occupied manifold or high in # the unoccupied manifold. #frequency_low_cutoff 200.0 # # Frequency step for full-frequency integration for the linear grid # Should be converged (the smaller, the better). # For molecules, delta_frequency should be the same as broadening. # Defaults to the value of broadening. #delta_frequency 0.1 # # Number of frequencies on the imaginary axis for method 2. #number_imaginary_freqs 15 # # Upper limit of the non-uniform frequency grid. # Defaults to 4*[[frequency_low_cutoff]] #frequency_high_cutoff 1000.0 # # Increase in the frequency step for the non-uniform frequency grid. #delta_frequency_step 1.0 # # Frequency step for the linear grid for the spectral function method. # Defaults to [[delta_frequency]]. #delta_sfrequency 0.1 # # Increase in frequency step for the non-uniform grid for the spectral function method. # Defaults to [[delta_frequency_step]] #delta_sfrequency_step 1.0 # # Upper bound for the linear grid for the spectral function method # and lower bound for the non-uniform frequency grid. # Defaults to [[frequency_low_cutoff]] #sfrequency_low_cutoff 200.0 # # Upper limit of the non-uniform frequency grid for the spectral function method. # Defaults to [[frequency_low_cutoff]] #sfrequency_high_cutoff 200.0 # Parameters for static subspace approximation (works only in the case of Full frequency Contour-Deformation formalism # frequency_dependence 2 and frequency_dependence_method 2). The method allows to speed-up a full frequency calculation by # expanding the frequency dependent part of the polarizability in the subspace formed by the lowest eigenvectors of the # static polarizability. # # # Activate the subspace approximation and define the screening threshold for the eigenvalues of the static polarizability #chi_eigenvalue_cutoff 1.0d-3 # # Define a fixed number of eigenvector to be used #nbasis_subspace -1 # # Write the subspace matrices in `eps0mat` and `epsmat` files instead of the full matrices #write_subspace_epsinv # # Discharge the output of the full static epsilon matrix in the eps0mat and epsmat file #subspace_dont_keep_full_eps_omega0 # # If ELPA is linked, specify to use ELPA for the diagonalization of the static polarizability #subspace_use_elpa # Logging convergence of the head & tail of polarizability matrix with respect to conduction bands. # Set to -1 for no convergence test # Set to 0 for the 5 column format including the extrapolated values (default). # Set to 1 for the 2 column format, real part only. # Set to 2 for the 2 column format, real and imaginary parts. #full_chi_conv_log -1 # qx qy qz 1/scale_factor is_q0 # # scale_factor is for specifying values such as 1/3 # is_q0 = 0 for regular, non-zero q-vectors (read val WFNs from `WFN`) # is_q0 = 1 for a small q-vector in semiconductors (read val WFNs from `WFNq`) # is_q0 = 2 for a small q-vector in metals (read val WFNs from `WFN`) # if present the small q-vector should be first in the list # You can generate this list with `kgrid.x`: just set the shifts to zero and use # same grid numbers as for `WFN`. Then replace the zero vector with q0. # begin qpoints 0.000000 0.000000 0.005000 1.0 1 0.000000 0.000000 0.062500 1.0 0 0.000000 0.000000 0.125000 1.0 0 0.000000 0.000000 0.187500 1.0 0 0.000000 0.000000 0.250000 1.0 0 0.000000 0.000000 0.312500 1.0 0 0.000000 0.000000 0.375000 1.0 0 0.000000 0.000000 0.437500 1.0 0 0.000000 0.000000 0.500000 1.0 0 0.000000 0.000000 0.562500 1.0 0 0.000000 0.000000 0.625000 1.0 0 0.000000 0.000000 0.687500 1.0 0 0.000000 0.000000 0.750000 1.0 0 0.000000 0.000000 0.812500 1.0 0 0.000000 0.000000 0.875000 1.0 0 0.000000 0.000000 0.937500 1.0 0 end # Scissors operator (linear fit of the quasiparticle # energy corrections) for the bands in WFN and WFNq. # For valence-band energies: # ev_cor = ev_in + evs + evdel * (ev_in - ev0) # For conduction-band energies: # ec_cor = ec_in + ecs + ecdel * (ec_in - ec0) # Defaults below. evs, ev0, ecs, ec0 are in eV. # If you have eqp.dat and eqp_q.dat files # this information is ignored in favor of the eigenvalues # in eqp.dat and eqp_q.dat. # One can specify all parameters for scissors operator # in a single line with cvfit (evs ev0 evdel ecs ec0 ecdel) # # #evs 0.0 #ev0 0.0 #evdel 0.0 #ecs 0.0 #ec0 0.0 #ecdel 0.0 # #cvfit 0.0 0.0 0.0 0.0 0.0 0.0 # Set this to use eigenvalues in eqp.dat and eqp_q.dat # If not set, these files will be ignored. #eqp_corrections # Write the bare Coulomb potential $v(q+G)$ to file #write_vcoul # Matrix Element Communication Method (Chi Sum Comm). Default is [[gcomm_matrix]] # which is good if $nk, nc, nv > nmtx, nfreq$. If $nk, nc, nv < nfreq, nmtx$ # ($nk, nv < nfreq$ since $nc \sim nmtx$), use gcomm_elements. Only [[gcomm_elements]] # is supported with the spectral method. # # #gcomm_matrix #gcomm_elements # Within gcomm_matrix, performs a non-blocking cyclic communication scheme # overlapping computation and communication in the evaluation of the polarizability # (reduce the time spent communication for large run, but require more memory) #comm_nonblocking_cyclic # In the case of static subspace approximation using comm_nonblocking_cyclic # tells the algorithm not to keep a fixed buffer sizes for communication, # in general not a good idea, little saving in term of memory #dont_keep_fix_buffers # In the case of static subspace replicate eigenvectors using collective operation, # performs in general worse than point to point, to be used mainly for debugging #sub_collective_eigen_redistr # Number of pools for distribution of valence bands # The default is chosen to minimize memory in calculation #number_valence_pools 1 # By default, the code computes the polarizability matrix, constructs # the dielectric matrix, inverts it and writes the result to file epsmat. # Use keyword skip_epsilon to compute the polarizability matrix and # write it to file chimat. Use keyword skip_chi to read the polarizability # matrix from file chimat, construct the dielectric matrix, invert it and # write the result to file epsmat. # # #skip_epsilon #skip_chi # Use traditional simple binary format for epsmat/eps0mat instead of HDF5 file format. # Relevant only if code is compiled with HDF5 support. #dont_use_hdf5 # Verbosity level, options are: # 1 = default # 2 = medium - info about k-points, symmetries, and eqp corrections. # 3 = high - full dump of the reduced and unfolded k-points. # 4 = log - log of various function calls. Use to debug code. # 5 = debug - extra debug statements. Use to debug code. # 6 = max - only use if instructed to, severe performance downgrade. # Note that verbosity levels are cumulative. Most users will want to stick # with level 1 and, at most, level 3. Only use level 4+ if debugging the code. #verbosity 1 # (Full Frequency only) Calculates several frequencies in parallel. No "new" # processors are used here, the chi summation is simply done in another order # way to decrease communication. This also allows the inversion of multiple # dielectric matrices simultaneously via ScaLAPACK, circumventing ScaLAPACK's # scaling problems. Can be very efficient for system with lots of G-vectors and when # you have many frequencies. In general gives speedup. However, in order to # calculate N frequencies in parallel, the memory to store `pol%gme` is currently # multiplied by N as well. # #nfreq_group 1 # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY # 'unfolded BZ' is from the kpoints in the WFN file # 'full BZ' is generated from the kgrid parameters in the WFN file # See comments in Common/checkbz.f90 for more details # # # Replace unfolded BZ with full BZ #fullbz_replace # Write unfolded BZ and full BZ to files #fullbz_write # The requested number of bands cannot break degenerate subspace # Use the following keyword to suppress this check # Note that you must still provide one more band in # wavefunction file in order to assess degeneracy #degeneracy_check_override # Instead of using the RHO FFT box to perform convolutions, we automatically # determine (and use) the smallest box that is compatible with your epsilon # cutoff. This also reduces the amount of memory needed for the FFTs. # Although this optimization is safe, you can disable it by uncommenting the # following line: #no_min_fftgrid # Uncomment this flag if you would like to restart your Epsilon calculation # instead of starting it from scratch. Note that we can only reuse q-points # that were fully calculated. This flag is ignored unless you are running # the code with HDF5. #restart # Q-grid for the epsmat file. Defaults to the WFN k-grid. #qgrid 0 0 0 # Use this option to generate an eps0mat file suitable for subsampled Sigma # calculations. The only thing this flag does is to allow a calculation with # more than one $q\rightarrow0$ points without complaining. #subsample

Epsilon/epsconv.inp

#---------------------------- # Example epsconv.inp for epsbinasc/epsascbin. # number of q-points # output filename # number of input files (will be merged) # input filenames 1 epsmat.out 1 epsmat.in

Epsilon/epsomega.inp

eps0mat ! epsmat file, full-frequency or static RHO ! RHO file for Plasmon-Pole 0.0 0.0 0.0 ! q-vector in crystal coordinates 1 0 0 ! G-vector in crystal coordinates 1 0 0 ! G`-vector in crystal coordinates 201 ! nFreq, for static epsmat. For full-freq., overwritten from file 0.5 ! dDeltaFreq in eV, in case of static epsmat. See above. 2.0 ! dBrdning in eV, in case of static epsmat. See above. epsPP.dat ! Plasmon-Pole epsilon, Re and Im parts epsR.dat ! Retarded epsilon, Re and Im parts epsA.dat ! Advanced epsilon, Re and Im parts

Epsilon/epsinvomega.inp

eps0mat(.h5) ! epsmat file, full-frequency or static RHO ! RHO file for Plasmon-Pole 0.0 0.0 0.0 ! q-vector in crystal coordinates 1 0 0 ! G-vector in crystal coordinates 1 0 0 ! G`-vector in crystal coordinates 201 ! nFreq, for static epsmat. For full-freq., overwritten from file 0.5 ! dDeltaFreq in eV, in case of static epsmat. See Above. 2.0 ! dBrdning in eV, in case of static epsmat. See Above. 0.1 ! Exciton binding energy to use to calculate the effective eps^-1 head for BSE. epsInvPP.dat ! Plasmon-Pole epsilon inverse, Re and Im parts epsInvR.dat ! Retarded epsilon inverse, Re and Im parts epsInvA.dat ! Advanced epsilon inverse, Re and Im parts

Epsilon/epsmat_merge.inp

44 7 ! ecuts1, nqtot 0.0000 0.0000 0.5000 1.0 ! qx qy qz div 0.0000 0.2500 0.0000 1.0 0.0000 0.2500 0.5000 1.0 0.0000 0.5000 0.0000 1.0 0.0000 0.5000 0.5000 1.0 0.2500 0.5000 0.0000 1.0 0.2500 0.5000 0.5000 1.0 1 ! nfiles epsmat ! filename(i), i=1,nfiles

Epsilon/epsmat_old2hdf5.inp

epsmat ! Name of input file epsmat.h5 ! Name of output file WFN ! Name of wave function file to extract header from icutv ! truncation flag (0=no truncation, 2=spherical, 4=wire, 5=box, 6=slab) truncval ! truncation radius, for spherical truncation. Otherwise, ignored

Sigma

Sigma/README

================================================================================ GW code: Sigma ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (September, 2011) Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 S. Ismail-Beigi (2002) Version 0.1 G. M. Rignanese, E. Chang, X. Blase (1998) Version 0.0 M. Hybertsen (1985) ------------------------------------------------------------------------------- Description: Sigma is the second half of the GW code. It should be run after calculating epsmat/esp0mat in Epsilon. It gives the quasiparticle self-energies and dispersion relation for quasielectron and quasihole states. The main result is written to sigma.log file. ------------------------------------------------------------------------------- Required Input: sigma.inp Input parameters. See example in this directory. epsmat(.h5) Inverse dielectric matrix (q<>0). Created using Epsilon. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). eps0mat(.h5) Inverse dielectric matrix (q->0). Created using Epsilon. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). WFN_inner Real or complex wavefunctions. k-grid should be the same as the q-grid of epsmat, though there can be a shift. This is usually the reduced points from an unshifted grid. RHO Charge density (only needed for generalized plasmon-pole model), from SCF calculation on which WFN_inner is based. vxc.dat Matrix elements of the exchange-correlation potential, from a mean-field calculation or a previous Sigma run. VXC file may be used instead via keyword dont_use_vxcdat. Additional Input: WFN_outer Outer wavefunctions between which the self-energy operator and exchange-correlation potential are sandwiched. If absent inner wavefunctions will be used instead. Note that VXC should be consistent with outer wfn while RHO with inner wfn. If outer wfn is generated using a hybrid functional, VXC contains the local part of exchange-correlation potential. In this case set bare_exchange_fraction in sigma.inp to compensate for the non-local part, or use vxc.dat instead of VXC. The file below will be read only if eqp_corrections is set in sigma.inp. eqp.dat A list of quasiparticle energy corrections for the bands in WFN_inner. The corrected eigenvalues are used for constructing the self-energy operator. The file below will be read only if eqp_outer_corrections is set in sigma.inp. eqp_outer.dat A list of quasiparticle energy corrections for the bands in WFN_outer. The corrected eigenvalues determine the energies at which the self-energy operator is calculated. vxc2.dat Matrix elements of the exchange-correlation potential, from a mean-field calculation or a previous Sigma run. This is for a one-shot hybrid functional like calculation instead of a Sigma calculation. VXC2 file may be used instead via keyword dont_use_vxc2dat. Auxiliary Files: x.dat Matrix elements of the bare exchange, generated by a previous Sigma run to speed up subsequent calculations. Read if use_xdat keyword is present, written otherwise. VXC Exchange-correlation potential (whose matrix elements are subtracted from DFT eigenvalues). Produced by mean-field code, from SCF calculation on which WFN_inner is based (or WFN_outer, if present). Used only if vxc.dat is not present or keyword dont_use_vxcdat is set. VXC2 Exchange-correlation potential (whose matrix elements are added to the hybrid functional like exchange). Produced by mean-field code, from SCF calculation on which WFN_inner is based (or WFN_outer, if present). Used only if vxc2.dat is not present or keyword dont_use_vxc2dat is set. ------------------------------------------------------------------------------- sigma.inp Please see example sigma.inp in this directory for complete options. ------------------------------------------------------------------------------- Output Files: The file below will be read only if eqp_corrections is set in sigma.inp. eqp0.dat Contains the on-shell QP energies = Emf - Vxc - Sig(Eo) This is *not* the recommended quantity to use for QP properties. This is Eqn. 36 from Hybertsen & Louie PRB 34 5390. eqp1.dat Contains the off-shell solution to the linearized Dyson`s equation = Eqp0 + (dSig/dE) / (1 - dSig/dE) * (Eqp0 - Eo), or a full linear interpolation if more freq. points where computed. This is the recommended quantity to use for QP properties. If you only evaluate Sigma at two frequencies, this is Eqn. 37 from Hybertsen & Louie PRB 34 5390. If there are more frequencies available, the code uses them to find a better linearized solution. For GW calculations without plasmon-pole models, the code reports how many solutions to Dyson`s equation were found. sigma_hp.log The log file containing quasiparticle energy values for desired states. For a full-frequency calculation only the value for Sigma calculated at energy closest to the outer wavefunction eigenvalue is shown. The file spectrum.dat contains the full Sigma(E) spectra. ch_converge.dat Convergence of Coulomb-hole term with respect to empty orbitals. spectrum.dat The real and imaginary parts of Sigma as a function of energy. The energy grid is specified in sigma.inp. This file is only output in full-frequency calculations. Some general notes: * IM(SIGMA) was calculated using the same broadening as RE(SIGMA), while IM(SIGMA2) was calculated without any broadening. There are 2 Sigmas currently reported if doing a real axis calculation (frequency_dependence_method 0) 1. Sigma = SX + CH with no Broadening. We do the energy denominator integral analytically. 2. Sigma = X + COR with no broadening. We do the energy denominator integral analytically. For contour deformation (frequency_dependence_method 2) only X + COR is given. But spectrum.dat contains columns for contributions from the poles and imaginary axis integral * Ew is not the same as the frequencies specified in sigma.inp. Ew is the absolute off-shell quasiparticle energy, and it is *not* measured wrt the Fermi energy. The (physically meaningful) on-shell quasiparticle energy EQP is the solution of Dyson's equation: Ew = E_LDA - Vxc + Re[Sig(Ew)]. ------------------------------------------------------------------------------- A Note About the Wings of Epsilon (for Semiconductors Only): The wings of Chi have terms of the following form: < vk | e^(i(G+q)r) | ck+q >< ck+q | e^(-iqr) | vk > (1) The matrix element on the right is < u_ck+q | u_vk > where u is the periodic part of the Bloch function. From k.p perturbation theory, this matrix element is proportional to q. The matrix element on the left with a non-zero G is typically roughly a constant as a function of q for small q (q being a small addition to G). Thus for a general G-vector, Chi_wing(G,q) \propto q. This directly leads to the wings of the screened untruncated Coulomb interaction being proportional to 1/q. Note that this function changes sign as q -> -q. Thus, when treating the q=0 point, we set the value of the wing to zero (the average of its value in the mini-Brillouin zone (mBZ). For G-vectors on high-symmetry lines, some of the matrix elements on the left of (1) will be zero for q=0, and therefore proportional to q. For such cases, Chi_wing(G,q) \propto q^2, and the wings of the screened Coulomb interaction are constant as a function of q. However, setting the q->0 wings to zero still gives us, at worst, linear convergence to the final answer with increased k-point sampling, because the q->0 point represents an increasingly smaller area in the BZ. Thus, we still zero out the q->0 wings, as discussed in A Baldereschi and E Tosatti, Phys. Rev. B 17, 4710 (1978). In the future, it may be worthwhile to have the user calculate chi / epsilon at two q-points (a third q-point at q=0 is known) in order to compute the linear and quadratic coefficients of each chi_wing(G,q) so that all the correct analytic limits can be taken. This requires a lot of messy code and more work for the user for only marginally better convergence with respect to k-points (the wings tend to make a small difference, and this procedure would matter for only a small set of the G-vectors). It is important, as always, for the user to converge their calculation with respect to both the coarse k-point grid used in sigma and kernel as well as with the fine k-point grid in absorption. ------------------------------------------------------------------------------- Tricks and hints: 1. Comments on convergence of scc (screened_coulomb_cutoff) and bcc (bare_coulomb_cutoff) The parameters scc and bcc are independent to each other and are related to the number or terms taken into account in the plane-wave expansion of Sigma_(SEX + COH) and V_xc, respectively. Since Sigma_(SEX) is related to epsilon, scc should be equal to or less than the epsilon_cutoff used to compute chi0 and epsilon. If you are to use large values for scc and bcc (say 50 Ry or so), a good suggestion is run the sigma code twice: first with large bcc and small scc, just to get x.dat and vxc.dat; then with large scc and any bcc, using the x.dat and vxc.dat files generated before. The second run is usually much faster than a run with large scc and bcc. 2. Metals If you are doing a metal you should report the shift used in sigma.inp whether using truncation or not. 3. Off-diagonal If you are doing off-diagonal matrix elements of Sigma use the utility offdiag in this directory to diagonalize the Sigma matrix. 4. Linear extrapolation for eqp1 If |eqp0 - ecor| > finite_difference_spacing linear extrapolation for eqp1 may be inaccurate. You should test the validity of eqp1 by rerunning calculation with self-energy evaluated at the eqp0 energies. For that, use the eqp_outer.dat file created with eqp.py script and point WFN_outer to WFN_inner (if you were not already using WFN_outer), i.e. run i) ln -s WFN_inner WFN_outer ii) ln -s eqp1.dat eqp_outer.dat and add eqp_outer_corrections to sigma.inp. If you get the same eqp1, the linearization looks good; if not, you can continue iterations like this to converge to the solution of the Dyson equation. 5. Utilities: ------------------------------------------------------------------------------- Sigma: QP shift and scissors paramters ------------------------------------------------------------------------------- TOOL: qp_shifts.py USAGE: qp_shift.py sigma_hp.log From sigma_hp.log file, writes two files which contain the LDA energies and the GW shifts (E_qp-E_lda) for that energy. Useful for determining scissor shifting parameters ecdel, evdel, etc. ------------------------------------------------------------------------------- Sigma: QP extraction ------------------------------------------------------------------------------- TOOL: eqp.py USAGE: eqp.py sigma_hp.log Extracts QP energies from sigma_hp.log file and generates file eqp.dat. This utility is currently deprecated, since the code writes the eqp0.dat and eqp1.dat automatically.

Sigma/sigma.inp

# sigma.inp # Energy cutoff for the screened Coulomb interaction, in Ry. The screened # Coulomb interaction $W_{GG'}(q)$ will contain all G-vectors with kinetic energy # $|q+G|^2$ up to this cutoff. Default is the epsilon_cutoff used in the # epsilon code. This value cannot be larger than the epsilon_cutoff or # the bare_coulomb_cutoff. #screened_coulomb_cutoff 35.0 # Energy cutoff for the bare Coulomb interaction, in Ry. The bare Coulomb # interaction $v(G+q)$ will contain all G-vectors with kinetic energy # $|q+G|^2$ up to this cutoff. Default is the WFN cutoff. #bare_coulomb_cutoff 60.0 # Total number of bands (valence+conduction) to sum over. Defaults to the # number of bands in the WFN file minus 1. #number_bands 1000 # Specify the Fermi level (in eV), if you want implicit doping # Note that value refers to energies AFTER scissor shift or eqp corrections. #fermi_level 0.0 # The Fermi level is treated as an absolute value # or relative to that found from the mean field (default) # # #fermi_level_absolute #fermi_level_relative # ### Specification of which matrix elements of $\Sigma$ to compute, # $\langle \psi_n | \Sigma(E_l) | \psi_m \rangle$. # # Note that $E_l$ is irrelevant for [[frequency_dependence]] -1 and 0. # # # Minimum band index for diagonal matrix elements of sigma (instead of [[diag]]) band_index_min 15 # Maximum band index for diagonal matrix elements of sigma (instead of [[diag]]) band_index_max 22 # # Number or diagonal matrix elements, i.e., for $n=m$. #number_diag ndiag # # Band indices for the diagonal matrix elements of Sigma ($n=m=l$) #begin diag # n_1 # n_2 # ... # n_ndiag #end # # # Number of off-diagonal matrix elements #number_offdiag noffdiag # # The off-diagonal matrix elements of Sigma # [[band_index_min]] <= n <= [[band_index_max]] # [[band_index_min]] <= m <= [[band_index_max]] # [[band_index_min]] <= l <= [[band_index_max]] # NOTE: the offdiag utility only works with the sigma_matrix syntax, below. #begin offdiag # n_1 m_1 l_1 # n_2 m_2 l_2 # ... # n_noffdiag m_noffdiag l_noffdiag #end # # # Alternatively, select a specific value of l and let n and m vary # in the range from band_index_min to band_index_max # Set l to 0 to skip the off-diagonal calculation (default) # If l = -1 then l_i is set to n_i (i = 1 ... noffdiag) # i.e. each row is computed at different eigenvalue # If l = -2 then l_i is set to m_i (i = 1 ... noffdiag) # i.e. each column is computed at different eigenvalue # For l > 0, all elements are computed at eigenvalue of band l. # Set t to 0 for the full matrix (default) # or to -1/+1 for the lower/upper triangle # #sigma_matrix l t # The range of spin indices for which Sigma is calculated # The default is the first spin component # # #spin_index_min 1 #spin_index_max 1 # What screening is present? (default = semiconductor). This is not used in Hartree-Fock # calculations (i.e., when [[frequency_dependence]] = -1.) # # # Gapped system screening_semiconductor # # Metallic system #screening_metal # # System with linear DOS at the Fermi level #screening_graphene # RECOMMENDED fast FFTW truncation schemes # The Coulomb Interaction is cutoff on the edges of # the Wigner-Seitz Cell in the non-periodic directions. # # # Truncation in all three directions #cell_box_truncation # # Trunctation along a1, a2 #cell_wire_truncation # # Trunctation along a3 #cell_slab_truncation # # Analytic, but non Wigner-Seitz cell, truncation #spherical_truncation # For Spherical Truncation, radius in Bohr #coulomb_truncation_radius 10.00 # Cutoff energy (in Ry) for averaging the Coulomb Interaction # in the mini-Brillouin Zones around the Gamma-point # without Truncation or for Cell Wire or Cell Slab Truncation. #cell_average_cutoff 1.0d-12 # Frequency dependence of the inverse dielectric matrix. # Set to -1 for the Hartree-Fock and hybrid functional approximation. # Set to 0 for the static COHSEX approximation. # Set to 1 for the Generalized Plasmon Pole model (default). # Set to 2 for the full frequency dependence. # Set to 3 for the Generalized Plasmon Pole model in the Godby-Needs flavor. # Note: does not work with parallelization in frequencies. # #frequency_dependence 1 # Full frequency dependence method for the polarizability. # set to 0 for the Real-Axis Integration method. # set to 2 for the Contour-Deformation method (default). #frequency_dependence_method 2 # For Full Frequency Calculations. # In order to evaluate Sigma(omega), you have to specify a frequency grid # for the frequencies omega. You can control where to center/shift the grid. # The options are: # 0 if you don't want any shift, i.e., omega is an absolute energy # 1 if you want to shift the first frequency omega=0 to the Fermi energy # (this was the default behavior in BerkeleyGW-1.0) # 2 if you want to center the frequency grid around each mean-field QP energy (default) #frequency_grid_shift 2 # If [[frequency_grid_shift]] is 2 (default), specify the frequency spacing # delta_frequency_eval in eV (default=0.2) and the width, in eV, of the # evaluation grid centered around each QP state (default=2.0). The code # will generate a frequency grid from -max_frequency_eval to max_frequency_eval. # You should increase the value of max_frequency_eval if you expect the # absolute QP corrections to be large, such as when dealing with molecules # (the code will warn if the frequency grid is too small). # Note for advanced users: the grids are actually centered around the outer # mean-field energies, so you can use WFN_outer and eqp_outer_corrections or # outer scissors parameters to fine-tune the frequency grid. # #delta_frequency_eval 0.2 #max_frequency_eval 2.0 # If [[frequency_grid_shift]] is 0 or 1, specify the initial frequency # init_frequency_eval (before the shift), in eV, the frequency spacing # delta_frequency_eval, in eV, and the number of frequency points # number_frequency_eval. # #init_frequency_eval 0.0 #delta_frequency_eval 0.1 #number_frequency_eval 501 # For Contour Deformation calculations, specify the integration method on the # imaginary axis (default is 0). Options are: # 0 for piecewise constant matrix elements centered at each imaginary frequency # 2 for piecewise quadratic matrix elements over each integration segment # 3 for cubic Hermite matrix elements over each integration segment #cd_integration_method 0 # Within the Contour Deformation formalism (frequency_dependence=2 ; frequency_dependence_method=2), # if the inverse dielectric matrix has been calculated with the static subspace method, # this flag activate the subspace calulation also for sigma (note that in this case even if you # keep the full epsilon matrix at omega zero, the calculation will be perfomed in the subspace). # Using or not such flag should NOT produce any difference in the final results (or very small due to roundoff), # but the code should be much faster. The implementation is different than the standard CD, making # use of zgemm/dgemm calls # #do_sigma_subspace # For Generalized Plasmon Pole. # The matrix element of the self-energy operator is # expanded to first order in the energy around Ecor. # # # Finite difference form for numerical derivative of Sigma. # grid = -3 : Calculate Sigma(w) on a grid, using the same frequency grid as # in full-frequency calculations. # none = -2 : dSigma/dE = 0 [skip the expansion]. # backward = -1 : dSigma/dE = (Sigma(Ecor) - Sigma(Ecor-dE)) / dE # central = 0 : dSigma/dE = (Sigma(Ecor+dE) - Sigma(Ecor-dE)) / (2*dE) # forward = 1 : dSigma/dE = (Sigma(Ecor+dE) - Sigma(Ecor)) / dE # default = 2 : forward for diagonal and none for off-diagonal #finite_difference_form 2 # # dE is finite difference spacing given in eV (defaults to 1.0) #finite_difference_spacing 1.0 # For Hartree-Fock/hybrid functional, no epsmat/eps0mat files are needed. # Instead provide a list of q-points and the grid size. # The list of q-points should not be reduced with time # reversal symmetry - because BerkeleyGW never uses time # reversal symmetry to unfold the q/k-points. Instead, # inversion symmetry does the job in the real version of # the code. # You can generate this list with kgrid.x: just set the shifts to zero and use # same grid numbers as for WFN_inner. # # # qx qy qz 1/scale_factor is_q0 # # Reduced coordinates of q-points. # scale_factor is for specifying values such as 1/3 # is_q0 indicated whether a q-point is Gamma (1) or not (0) #begin qpoints # 0.0 0.0 0.0 1.0 1 #end # # The regular grid of q-points corresponding to the list. #qgrid 1 1 1 # What should we do when we perform a HL-GPP or a GN-GPP calculations and we # find an invalid mode frequency with $\omega_{GG'}^2 < 0$ Options are: # -1: Default, same as 3. # 0: Skip invalid mode and ignore its contribution to the self energy. # 1: "Find" a purely complex mode frequency. This was the default behavior in BGW-1.x. # 2: Set the mode frequency to a fixed value of 2 Ry. # 3: Treat that mode within the static COHSEX approximation (move frequency to infinity). #invalid_gpp_mode -1 # Add remainder from tail of epsilon for full frequency. #use_epsilon_remainder # Logging the convergence of the CH term with respect to the number of bands # in the output file "ch_converge.dat". Options are: # 0 to log only the real part of VBM, CBM and the gap (default). # 1 to log the real and imag. parts of all bands for which we compute Sigma. # #full_ch_conv_log 0 # Use precalculated matrix elements of bare exchange from x.dat. # The default is not to use them. #use_xdat # Do not use precalculated matrix elements of exchange-correlation from vxc.dat. # The default is to use them. #dont_use_vxcdat # Read from traditional simple binary format for epsmat/eps0mat instead of HDF5 file format. # Relevant only if code is compiled with HDF5 support. #dont_use_hdf5 # Fraction of bare exchange. # Set to 1.0 if you use the exchange-correlation matrix elements # read from file vxc.dat. Set to 1.0 for local density functional, # 0.0 for HF, 0.75 for PBE0, 0.80 for B3LYP if you use the local # part of the exchange-correlation potential read from file VXC. # For functionals such as HSE whose nonlocal part is not some # fraction of bare exchange, use vxc.dat and not this option. # This is set to 1.0 by default. # #bare_exchange_fraction 1.0 # Broadening for the energy denominator in CH and SX within GPP. # If it is less than this value, the sum is better conditioned than # either CH or SX directly, and will be assigned to SX while CH = 0. # This is given in eV, the default value is 0.5 # #gpp_broadening 0.5 # Cutoff for the poles in SX within GPP. # Divergent contributions that are supposed to sum to zero are removed. # This is dimensionless, the default value is 4.0 #gpp_sexcutoff 4.0 # kx ky kz 1/scale_factor # # scale_factor is for specifying values such as 1/3 begin kpoints 0.0000 0.0000 0.0000 1.0 end # Scissors operator (linear fit of the quasiparticle # energy corrections) for the bands in WFN_inner # For valence-band energies: # ev_cor = ev_in + evs + evdel * (ev_in - ev0) # For conduction-band energies: # ec_cor = ec_in + ecs + ecdel * (ec_in - ec0) # Defaults below. evs, ev0, ecs, ec0 are in eV # # #evs 0.0 #ev0 0.0 #evdel 0.0 #ecs 0.0 #ec0 0.0 #ecdel 0.0 # # One can specify all parameters for scissors operator # in a single line as (evs ev0 evdel ecs ec0 ecdel) #cvfit 0.0 0.0 0.0 0.0 0.0 0.0 # Scissors operator (linear fit of the quasiparticle # energy corrections) for the bands in WFN_outer. # Has no effect if WFN_outer is not supplied. # For valence-band energies: # ev_cor = ev_in + evs_outer + evdel_outer * (ev_in - ev0_outer) # For conduction-band energies: # ec_cor = ec_in + ecs_outer + ecdel_outer * (ec_in - ec0_outer) # Defaults below. evs_outer, ev0_outer, ecs_outer, ec0_outer are in eV # # #evs_outer 0.0 #ev0_outer 0.0 #evdel_outer 0.0 #ecs_outer 0.0 #ec0_outer 0.0 #ecdel_outer 0.0 # # One can specify these parameters in a single line # as (evs_outer ev0_outer evdel_outer ecs_outer ec0_outer ecdel_outer) #cvfit_outer 0.0 0.0 0.0 0.0 0.0 0.0 # Set this to use eigenvalues in eqp.dat # If not set, this file will be ignored. #eqp_corrections # # Set this to use eigenvalues in eqp_outer.dat # If not set, this file will be ignored. # Has no effect if WFN_outer is not supplied. #eqp_outer_corrections # The average potential on the faces of the unit cell # in the non-periodic directions for the bands in WFN_inner # This is used to correct for the vacuum level # The default is zero, avgpot is in eV # #avgpot 0.0 # The average potential on the faces of the unit cell # in the non-periodic directions for the bands in WFN_outer # This is used to correct for the vacuum level. # Has no effect if WFN_outer is not supplied. # The default is zero, avgpot_outer is in eV # #avgpot_outer 0.0 # Write the bare Coulomb potential $v(q+G)$ to file #write_vcoul # Number of pools for parallel sigma calculations # The default is chosen to minimize memory in calculation #number_sigma_pools 1 # Threshold for considering bands degenerate, for purpose of # making sure all of degenerate subspaces are included, # for band-averaging, and for setting offdiagonals to zero by symmetry. (Ry) #tol_degeneracy 1e-6 # Verbosity level, options are: # 1 = default # 2 = medium - info about k-points, symmetries, and eqp corrections. # 3 = high - full dump of the reduced and unfolded k-points. # 4 = log - log of various function calls. Use to debug code. # 5 = debug - extra debug statements. Use to debug code. # 6 = max - only use if instructed to, severe performance downgrade. # Note that verbosity levels are cumulative. Most users will want to stick # with level 1 and, at most, level 3. Only use level 4+ if debugging the code. # #verbosity 1 # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY # 'unfolded BZ' is from the kpoints in the WFN_inner file # 'full BZ' is generated from the kgrid parameters in the WFN_inner file # See comments in Common/checkbz.f90 for more details # # # Replace unfolded BZ with full BZ #fullbz_replace # # Write unfolded BZ and full BZ to files #fullbz_write # The requested number of bands cannot break degenerate subspace # Use the following keyword to suppress this check # Note that you must still provide one more band in # wavefunction file in order to assess degeneracy #degeneracy_check_override # The sum over q-points runs over the full Brillouin zone. # For diagonal matrix elements between non-degenerate bands # and for spherically symmetric Coulomb potential (no truncation # or spherical truncation), the sum over q-points runs over # the irreducible wedge folded with the symmetries of # a subgroup of the k-point. The latter is the default. # In both cases, WFN_inner should have the reduced k-points # from an unshifted grid, i.e. same as q-points in Epsilon. # With no_symmetries_q_grid, any calculation can be done; # use_symmetries_q_grid is faster but only diagonal matrix elements # of non-degenerate or band-averaged states can be done. # # #no_symmetries_q_grid #use_symmetries_q_grid # If no_symmetries_q_grid is used, this flag skips the averaging # of the degenerate subspace. This might be useful for treating accidental # degeneracies. #dont_symmetrize # Off-diagonal elements are zero if the two states belong to # different irreducible representations. As a simple proxy, # we use the size of the degenerate subspaces of the two states: # if the sizes are different, the irreps are different, and the # matrix element is set to zero without calculation. # Turn off this behavior for testing by setting flag below. # Using WFN_outer effectively sets no_symmetries_offdiagonals. # #no_symmetries_offdiagonals # Rotation of the k-points may bring G-vectors outside of the sphere. # Use the following keywords to specify whether to die if some of # the G-vectors fall outside of the sphere. The default is to die. # Set to die in case screened_coulomb_cutoff = epsilon_cutoff. # Set to ignore in case screened_coulomb_cutoff < epsilon_cutoff. # # #die_outside_sphere #ignore_outside_sphere # Dealing with the convergence of the CH term. # Set to 0 to compute a partial sum over empty bands. # Set to 1 to compute the exact static CH. # In case of exact_static_ch = 1 and frequency_dependence = 1 (GPP) or 2 (FF), # the partial sum over empty bands is corrected with the static remainder # which is equal to 1/2 * (exact static CH - partial sum static CH), # additional columns in sigma_hp.log labeled ch', sig', eqp0', eqp1' # are computed with the partial sum without the static remainder, # and ch_converge.dat contains the static limit of the partial sum. # In case of exact_static_ch = 0 and frequency_dependence = 0 (COHSEX), # columns ch, sig, eqp0, eqp1 contain the exact static CH, # columns ch', sig', eqp0', eqp1' contain the partial sum static CH, # and ch_converge.dat contains the static limit of the partial sum. # For exact_static_ch = 1 and frequency_dependence = 0 (COHSEX), # columns ch', sig', eqp0', eqp1' are not printed and # file ch_converge.dat is not written. # Default is 0 for frequency_dependence = 1 and 2; # 1 for frequency_dependence = 0; # has no effect for frequency_dependence = -1. # It is important to note that the exact static CH answer # depends not only on the screened Coulomb cutoff but also on the bare Coulomb cutoff # because G-G' for G's within the screened Coulomb cutoff can be outside the screened # Coulomb cutoff sphere. And, therefore, the bare Coulomb cutoff sphere is used. #exact_static_ch 0 # Do not average W over the minibz, and do not replace the head of eps0mat with # averaged value. #skip_averagew # By default, the code reads the dielectric matrix for a single q->0 q-point. # The following flag enables the subsampling of Voronoi cell containing Gamma. # Your eps0mat file should contain a list of radial q-points (which will not be # unfolded by symmetries) instead of a single q->0 point. You should provide a # file subweights.dat containing the weights w(q) associated to each subsampled # q-point (which will be renormalized so that \sum w(q)=1). # Using this subsampling allows one to accelerate the convergence with respect # to the number of q-points, and is especially helpful when dealing with # large unit cells, truncated Coulomb potential and birefringent materials. # #subsample

Sigma/sig2wan.inp

sigma_hp.log ! Sigma output file to read k-points, eigenvalues and symmetries from 1 ! spin component to read from sigma_hp.log file 1 ! set to 0 or 1 to read eqp0 or eqp1 from sigma_hp.log file prefix.nnkp ! Wannier90 input file to read k-points from prefix.eig ! file where the output of sig2wan is written nbands ! number of bands to write out

BSE

BSE/README_kernel

================================================================================ BSE code: Kernel ================================================================================ Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze. Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 C. Spataru, S. Ismail-Beigi (2004) Version 0.1 M. L. Tiago, E. Chang, G. M. Rignanese (1999) -------------------------------------------------------------------------------- Description: This code constructs the direct and exchange Kernel matrix on the coarse grid. This is done essentially by computing Eqs 34, 35 and 42-46 of Rohlfing and Louie. -------------------------------------------------------------------------------- Required Input: kernel.inp Input parameters. See detailed explanation below. WFN_co Wavefunctions on coarse grid. Recommended: use an unshifted grid of the same size as the q-grid in epsmat. Shift will increase number of q-vectors needed in epsmat. epsmat(.h5) Inverse dielectric matrix (q<>0). Created using Epsilon. Must contain the all q=k-k' generated from WFN_co, including with symmetry if use_symmetries_coarse_grid is set. The file has a ".h5" extension if the code was built with HDF5 support. eps0mat(.h5) Inverse dielectric matrix (q->0). Created using Epsilon. The file has a ".h5" extension if the code was built with HDF5 support. Note Kernel does not require quasiparticle eigenvalues. It may be run in parallel with Sigma. -------------------------------------------------------------------------------- kernel.inp Please see example kernel.inp in this directory for more complete options. -------------------------------------------------------------------------------- Output Files: bsedmat Direct kernel matrix elements on unshifted coarse grid. bsexmat Exchange kernel matrix elements on unshifted coarse grid. or bsemat.h5 Includes data from both of above if compiled with HDF5 support. For specification, see bsemat.h5.spec. Note that you can use the bsemat_hdf5_upgrade.py utility to upgrade a bsemat.h5 file generated with BerkeleyGW prior to 1.2 (r6974). -------------------------------------------------------------------------------- A Note About the Wings of Epsilon (for Semiconductors Only): The wings of Chi have terms of the following form: < vk | e^(i(G+q)r) | ck+q >< ck+q | e^(-iqr) | vk > (1) The matrix element on the right is < u_ck+q | u_vk > where u is the periodic part of the Bloch function. From k.p perturbation theory, this matrix element is proportional to q. The matrix element on the left with a non-zero G is typically roughly a constant as a function of q for small q (q being a small addition to G). Thus for a general G-vector, Chi_wing(G,q) \propto q. This directly leads to the wings of the screened untruncated Coulomb interaction being proportional to 1/q. Note that this function changes sign as q -> -q. Thus, when treating the q=0 point, we set the value of the wing to zero (the average of its value in the mini-Brillouin zone (mBZ). For G-vectors on high-symmetry lines, some of the matrix elements on the left of (1) will be zero for q=0, and therefore proportional to q. For such cases, Chi_wing(G,q) \propto q^2, and the wings of the screened Coulomb interaction are constant as a function of q. However, setting the q->0 wings to zero still gives us, at worst, linear convergence to the final answer with increased k-point sampling, because the q->0 point represents an increasingly smaller area in the BZ. Thus, we still zero out the q->0 wings, as discussed in A Baldereschi and E Tosatti, Phys. Rev. B 17, 4710 (1978). In the future, it may be worthwhile to have the user calculate chi / epsilon at two q-points (a third q-point at q=0 is known) in order to compute the linear and quadratic coefficients of each chi_wing(G,q) so that all the correct analytic limits can be taken. This requires a lot of messy code and more work for the user for only marginally better convergence with respect to k-points (the wings tend to make a small difference, and this procedure would matter for only a small set of the G-vectors). It is important, as always, for the user to converge their calculation with respect to both the coarse k-point grid used in sigma and kernel as well as with the fine k-point grid in absorption. -JRD+MJ -------------------------------------------------------------------------------- Tricks and hints: 1. To optimize distribution of work among PEs, do the following: Choose processors to divide: nk^2 (if npes < nk^2) nk^2*nc^2 (if npes < nk^2*nc^2) nk^2*nc^2*nv^2 (if npes < nk^2*nc^2*nv^2) 2. All input and output files (except kernel.inp) are in binary format. 3. The interaction matrices are calculated in full! i.e. not only the upper triangle. In diag, currently only the upper triangle is used. 4. The Brillouin zone is built using a Wigner-Seitz construction, this way the head matrix elements are easily calculated. 5. The dielectric matrix is by default stored in memory. 6. The parameters scc (screened_coulomb_cutoff) and bcc (bare_coulomb_cutoff) are the same as scc and bcc used in Simga. The parameters scc and bcc should be equal to or less than the epsilon_cutoff and wavefunction_cutoff used in Epsilon and DFT, respectively. See Sigma/README for more details. Converters from old versions of file formats to current version are available in version 2.4.

BSE/kernel.inp

# kernel.inp # specify the number of valence bands (counting down from HOMO) number_val_bands 3 # conduction bands (counting up from LUMO) number_cond_bands 3 # Energy cutoff for the screened Coulomb interaction, in Ry. The screened # Coulomb interaction W_{GG`}(q) will contain all G-vectors with kinetic energy # |q+G|^2 up to this cutoff. Default is the epsilon_cutoff used in the # epsilon code. This value cannot be larger then the epsilon_cutoff or # the bare_coulomb_cutoff. #screened_coulomb_cutoff 35.0 # Energy cutoff for the bare Coulomb interaction, in Ry. The bare Coulomb # interaction v(G+q) will contain all G-vectors with kinetic energy # |q+G|^2 up to this cutoff. Default is the WFN cutoff. #bare_coulomb_cutoff 60.0 # Specify the Fermi level (in eV), if you want implicit doping # Note that value refers to energies AFTER scissor shift or eqp corrections. #fermi_level 0.0 # The Fermi level is treated as an absolute value # or relative to that found from the mean field (default) #fermi_level_absolute #fermi_level_relative # What screening is present? (default = semiconductor) screening_semiconductor #screening_metal #screening_graphene # this is for a system with linear DOS at the Fermi level # RECOMMENDED fast FFTW truncation schemes # The Coulomb Interaction is cutoff on the edges of # the Wigner-Seitz Cell in the non-periodic directions # Periodic directions are a1,a2 for slabs and a3 for wires #cell_box_truncation #cell_wire_truncation #cell_slab_truncation # Analytic, but non Wigner-Seitz cell, truncation #spherical_truncation # For Spherical Truncation, radius in Bohr #coulomb_truncation_radius 10.00 # Flag for coarse grid of k-points in the BZ. # Should we unfold using symmetries? either # no_symmetries_coarse_grid (default) or # use_symmetries_coarse_grid. If you calculated # epsmat on a reduced q grid, you should use # symmetries here! #use_symmetries_coarse_grid no_symmetries_coarse_grid # Write the bare Coulomb potential V(q+G) to file #write_vcoul # Low communication # The default behavior of the code is to distribute the dielectric matrix # among the processors. While this minimizes memory usage, it also # increases the communication. By using the low_comm flag, each processor # will store the whole dielectric matrix. It is advisable to use this flag # whenever each PE has enough memory to hold the whole epsmat file. #low_comm # Low Memory option # Calculate matrix elements separately for each k,c,v,k',c',v' pair #low_memory # Use traditional simple binary format for bsedmat/bsexmat instead of HDF5 file format. # Relevant only if code is compiled with HDF5 support. #dont_use_hdf5 # Verbosity level, options are: # 1 = default # 2 = medium - info about k-points, symmetries, and eqp corrections. # 3 = high - full dump of the reduced and unfolded k-points. # 4 = log - log of various function calls. Use to debug code. # 5 = debug - extra debug statements. Use to debug code. # 6 = max - only use if instructed to, severe performance downgrade. # Note that verbosity levels are cumulative. Most users will want to stick # with level 1 and, at most, level 3. Only use level 4+ if debugging the code. #verbosity 1 # Request calculation of the Kernel using spinor wavefunctions #spinor # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY # High Memory option # Save all wavefunction FFTs when calculating the BSE kernel. # Overwrites the low_memory option. #high_memory # 'unfolded BZ' is from the kpoints in the WFN file # 'full BZ' is generated from the kgrid parameters in the WFN file # See comments in Common/checkbz.f90 for more details # Replace unfolded BZ with full BZ #fullbz_replace # Write unfolded BZ and full BZ to files #fullbz_write # Rotation of the k-points may bring G-vectors outside of the sphere. # Use the following keywords to specify whether to die if some of # the G-vectors fall outside of the sphere. The default is to ignore. # Set to die in case screened_coulomb_cutoff = bare_coulomb_cutoff. # Set to ignore in case screened_coulomb_cutoff < bare_coulomb_cutoff. #die_outside_sphere #ignore_outside_sphere # Flag to read k-points from the 'kpoints' file. # The default is to read k-points from the wfn file. #read_kpoints # Calculates the kernel for all n1n2,n1'n2' transitions, and not only the pairs # vc,v'c' given by the Tamm-Dancoff approximation (TDA). Notes: # 1) With this option BerkeleyGW will calculate transitions beyond those needed # by the full BSE (such as vv,cc). # 2) In principle, one should *always* calculate these extra kernel blocks, # because the interpolation routine in absorption mixes wavefunction # characters, in particular for metallic and narrow-gap semiconductors. # 3) You do not need these extended kernel blocks *only* if you are *not # interpolating* later on. However, the only way to do non-TDA absorption # calculation right now is with the extended kernel flag (i.e., there's no # intermediate option to include only vc,c'v' transitions but not vv,cc). # 4) Only parallelization over k^2 is supported. #extended_kernel

BSE/README_absorption

================================================================================ BSE code: Absorption ================================================================================ Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004) -------------------------------------------------------------------------------- Description: This code is the second half of the BSE code. It interpolates the coarse grid electron-hole kernel onto the fine grid and then diagonalized the BSE equation. The output is the electron-hole eigenfunctions and eigenvalues as well the absorption spectra. -------------------------------------------------------------------------------- Required Input: absorption.inp Input parameters. See detailed explanation below. WFN_fi Wavefunctions in unshifted fine grid (conduction and valence for momentum operator, conduction for velocity operator). WFNq_fi Wavefunctions in shifted fine grid (not needed for momentum operator, valence for velocity operator). WFN_co Wavefunctions on unshifted coarse grid. Must be the same as used for Kernel. eps0mat(.h5) Must be same as used in Kernel. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). epsmat(.h5) Must be same as used in Kernel. The file has a ".h5" extension if the code is compiled with HDF5 support (for specification, see epsmat.h5.spec). bsedmat BSE matrix elements in coarse grid, direct part. This should be generated with Kernel code using same WFN_co. bsexmat BSE exchange matrix elements. This should be generated with Kernel code using same WFN_co. or bsemat.h5 Includes data from both of above if compiled with HDF5 support. For specification, see bsemat.h5.spec. Note that you can use the bsemat_hdf5_upgrade.py utility to upgrade a bsemat.h5 file generated with BerkeleyGW prior to 1.2 (r6974). Additional Input: eqp.dat A list of quasiparticle energy corrections for the bands in WFN_fi. Used if eqp_corrections is set in absorption.inp. eqp_q.dat A list of quasiparticle energy corrections for the bands in WFNq_fi. Used if eqp_corrections is set in absorption.inp. eqp_co.dat A list of quasiparticle energy corrections for the bands in WFN_co. Used if eqp_co_corrections is set in absorption.inp. kpoints A list of k-points in unshifted fine grid. EXPERIMENTAL. If absent k-points from WFN_fi file are used. kpoints_co A list of k-points in unshifted coarse grid. EXPERIMENTAL. If absent k-points from WFN_co file are used. Auxiliary Files: (output files from previous runs - used as input to speed up calculation) dtmat Transformation matrices, dcc/dvv use for interpolation between coarse and fine grid. This file must be consistent with your bsedmat and bsexmat files and corresponding coarse and fine wavefunctions. NOTE: the file format for dtmat was changed in BerkeleyGW 1.1.0 (r5961) vmtxel Optical matrix elements (velocity or momentum) between single particle states. epsdiag.dat Diagonal elements of dielectric matrix on the q-grid. Must be consistent with epsmat and eps0mat. eigenvalues.dat Contains electron-hole eigenvalues and transition matrix elements. -------------------------------------------------------------------------------- absorption.inp Please see example absorption.inp in this directory for more complete options. -------------------------------------------------------------------------------- Output Files: eigenvalues.dat Has eigenvalues/transition matrix elements of e-h states, eigenvalues in eV, mtxels in atomic units. eigenvalues_noeh.dat As above but for non-interacting e-h transitions, showing k-point, bands, and spin for each. eigenvectors Has the excitonic wavefunctions in Bloch space: A_svck absorption_eh.dat Dielectric function and density of excitonic states. Four Columns energy (in eV) | epsilon_2 | epsilon_1 | DOS DOS is normalized (\int (DOS) d(omega) = 1) absorption_noeh.dat Non-interacting (RPA) dielectric function and joint density of states. Four columns: energy (in eV) | epsilon_2 | epsilon_1 | JDOS JDOS is normalized (\int (JDOS) d(omega) = 1) dvmat_norm.dat The norms of the dvv overlap matrices between the valence band k on the fine grid and the closest k-point on the coarse grid dcmat_norm.dat The norms of the dcc overlap matrices between the conduction band k on the fine grid and the closest k-point on the coarse grid eqp.dat, eqp_q.dat Quasiparticle corrections for WFN_fi and WFNq_fi interpolated from the coarse grid if eqp_co_corrections is used. bandstructure.dat Same as eqp.dat and eqp_q.dat but in a format suitable for plotting as a bandstructure. -------------------------------------------------------------------------------- Tricks and hints: 1. To optimize distribution of work among PEs, choose the number of PEs so that Nk*Nc*Nv in the fine grid is a multiple of the number of PEs. The parallelization is first done over over k-points. 2. The Brillouin zone is built using a Wigner-Seitz construction; this way the head matrix elements are easily calculated. 3. Check if the transformation matrices have norm close to 1! They are usually normalized (look at the end of intwfn.f90). The norms are in the files dvmat_norm.dat and dcmat_norm.dat. 4. Unfolding of irreducible BZ: if you want to skip the unfolding and use the set of k-points in WFN_fi as a sampling of the whole BZ, specify the no_symmetries_* options in absorption.inp. 5. The "number_eigenvalues" keyword: using this keyword tells the code to store only the first nn eigenvalues/eigenvectors. So far, this option is implemented only with the SCALAPACK diagonalization routines. 6. Analyzing eigenvectors. We have a tool called summarize_eigenvectors to read in and analyze eigenvectors for a group of exciton states. For specific states specified, it sums the total contribution from each k-point. Please see the example input summarize_eigenvectors.inp.

BSE/absorption.inp

# absorption.inp ########################################## # OPTIONS FOR BOTH ABSORPTION AND INTEQP # ########################################## # Number of occupied bands on fine (interpolated) k-point grid number_val_bands_fine 3 # Number of occupied bands on coarse (input) k-point grid number_val_bands_coarse 3 # Number of unoccupied bands on fine (interpolated) k-point grid number_cond_bands_fine 3 # Number of unoccupied bands on coarse (input) k-point grid number_cond_bands_coarse 3 # In metallic systems, PARATEC often outputs incorrect occupation # levels in wavefunctions. Use this to override these values. # lowest_occupied_band should be 1 unless you have some very # exotic situation. #lowest_occupied_band vmin #highest_occupied_band vmax # Specify the Fermi level (in eV), if you want implicit doping # Note that value refers to energies AFTER scissor shift or eqp corrections. # If the Fermi level is moved, then you must use both or neither # of eqp_corrections and eqp_co_corrections, or no interpolation. # NOTE: If you are using inteqp.x to interpolate eqp_co.dat into a eqp.dat # file that will be later used in absorption.x, shift the Fermi level only # in absorption.x, but not in inteqp.x. #fermi_level 0.0 # The Fermi level is treated as an absolute value # or relative to that found from the mean field (default) #fermi_level_absolute #fermi_level_relative # Scissors operator (linear fit of the quasiparticle # energy corrections) for the bands in WFN_fi and WFNq_fi. # For valence-band energies: # ev_cor = ev_in + evs + evdel * (ev_in - ev0) # For conduction-band energies: # ec_cor = ec_in + ecs + ecdel * (ec_in - ec0) # Defaults below. evs, ev0, ecs, ec0 are in eV #evs 0.0 #ev0 0.0 #evdel 0.0 #ecs 0.0 #ec0 0.0 #ecdel 0.0 # or #cvfit 0.0 0.0 0.0 0.0 0.0 0.0 # These flags define whether to use symmetries to unfold # the Brillouin zone or not in files WFN_fi (unshifted fine # grid), WFNq_fi (shifted fine grid), WFN_co (coarse grid). # Warning, the default is always not to unfold! # If your unshifted fine grid is reduced (most cases), # you will want to use symmetries here! #no_symmetries_fine_grid #use_symmetries_fine_grid # If your shifted fine grid is reduced (most cases), # you will want to use symmetries here! Note that # if you use symmetries in the unshifted grid you will # need to generate the shifted grid using the same # procedure as generating the shifted grid for an # epsilon calculation. i.e. use gw_shift in paratec # and a non-zero small q-shift in kgrid.inp #no_symmetries_shifted_grid #use_symmetries_shifted_grid # If you calculated the coarse grid on a reduced q-grid, # you should use symmetries here! #no_symmetries_coarse_grid #use_symmetries_coarse_grid # Regular grid used to calculate qpt_averages. # Default is the kgrid in the WFN_fi file. # It matters only if you want to perform minicell averages. #regular_grid n1 n2 n3 # How to calculate optical transition probabilities. # No default for absorption, one must be specified. # For inteqp, default is momentum. # For momentum and JDOS, only WFN_fi is used. # For velocity, the valence bands come from WFNq_fi. use_velocity #use_momentum # For Haydock there is also a third option to calculate # Joint density of states. Diagonalization computes this for free. #use_dos # Verbosity level, options are: # 1 = default # 2 = medium - info about k-points, symmetries, and eqp corrections. # 3 = high - full dump of the reduced and unfolded k-points. # 4 = log - log of various function calls. Use to debug code. # 5 = debug - extra debug statements. Use to debug code. # 6 = max - only use if instructed to, severe performance downgrade. # Note that verbosity levels are cumulative. Most users will want to stick # with level 1 and, at most, level 3. Only use level 4+ if debugging the code. #verbosity 1 # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY (ABSORPTION AND INTEQP) # 'unfolded BZ' is from the kpoints in the WFN file # 'full BZ' is generated from the kgrid parameters in the WFN file # See comments in Common/checkbz.f90 for more details # Replace unfolded BZ with full BZ #fullbz_replace # Write unfolded BZ and full BZ to files #fullbz_write # Flag to read k-points from the 'kpoints' file. # The default is to read k-points from the wfn file. #read_kpoints # This is needed only with read_kpoints and if you selected velocity operator above. # This should match the shift between WFN_fi and WFNq_fi. #q_shift s1 s2 s3 # The requested number of valence or conduction bands cannot break degenerate subspace. # Use the following keyword to suppress this check. # Note that you must still provide one more band in # wavefunction file in order to assess degeneracy. # For inteqp, only the coarse grid is checked. #degeneracy_check_override # Request calculation of the fully-relativistic form of the BSE, using spinor wavefunctions #spinor ##################################### # OPTIONS ONLY FOR ABSORPTION BELOW # ##################################### # Which algorithm do we use to solve the BSE? We can either do a full # diagonalization with ScaLAPACK or LAPACK) or use the # Haydock iterative solver. diagonalization #haydock # In adittion to the solver above, you can also use the Lanczos iterative # solver, which requires ScaLAPACK, but works with both TDA and full BSE. #lanczos # For the Lanczos scheme, you can specify whether you can do use the average # Gaussian quadrature, which typically speeds up convergence with respect # to the number of iterations by a factor of 2. The default is to use it. #lanczos_gauss_quadrature #no_lanczos_gauss_quadrature # What screening is present? (default = semiconductor) screening_semiconductor #screening_metal #screening_graphene # this is for a system with linear DOS at the Fermi level # Compute only the lowest neig eigenvalues/eigenvectors. # The default is to calculate all nv*nc*nk of them. # Only for diagonalization, not for haydock. #number_eigenvalues neig # If you are not performing full diagonalization (eg: if using Haydock), # you must specify the number of iterations. #number_iterations 100 # Set this to use eigenvalues in eqp.dat and eqp_q.dat # If not set, these files will be ignored. #eqp_corrections # Set this to use eigenvalues in eqp_co.dat # These quasiparticle corrections will be interpolated to # the shifted and unshifted fine grids and written to eqp.dat, # eqp_q.dat, and bandstructure.dat. If not set, this file will be ignored. #eqp_co_corrections # RECOMMENDED fast FFTW truncation schemes # The Coulomb Interaction is cutoff on the edges of # the Wigner-Seitz Cell in the non-periodic directions # Periodic directions are a1,a2 for slabs and a3 for wires #cell_box_truncation #cell_wire_truncation #cell_slab_truncation # Analytic, but non Wigner-Seitz cell, truncation #spherical_truncation # For Spherical Truncation #coulomb_truncation_radius 10.00 # Cutoff energy for averaging the Coulomb Interaction # in the Mini Brillouin Zones around the Gamma-point # without Truncation or for Cell Wire or Cell Slab Truncation. # The value is in Rydbergs, the default is 10^{-12} #cell_average_cutoff 1.0d-12 # This is needed if you selected momentum operator above. # This vector will be normalized in the code. #polarization p1 p2 p3 # If we have already calculated the optical matrix elements, # do we read them from file to save time? #read_vmtxel # Read 'eps2_moments' generated during previous run (Haydock only) #read_eps2_moments # Reduce cost of calculation if we've already computed # the eigensolutions. This reads the eigenvalues and # transition matrix elements from the file 'eigenvalues.dat' #read_eigenvalues # If we only want the non-interacting spectra (i.e. no electron- # hole interaction, RPA). Only WFN_fi and WFNq_fi are needed as inputs. # With the 'read_eigenvalues' flag, both absorption_eh.dat and # absorption_noeh.dat will be created. #noeh_only # If already calculated, read the interpolation matrices dvv # and dcc from file dtmat. #read_dtmat # Numerical broadening width and type for generating absorption spectrum. # Haydock only does Lorentzian. epsilon_1 is always Lorentzian. # The width is controlled by energy_resolution. energy_resolution 0.1 # epsilon_2 with diagonalization is Gaussian by default. You can also choose Lorentzian. #lorentzian_broadening gaussian_broadening # Frequency step (eV) for generating absorption spectrum. #delta_frequency 0.01 # The Gaussian and Voigt options are only available for epsilon_2 with diagonalization. # Voigt becomes Lorentzian at sigma -> 0 and Gaussian at gamma = 0. # Note that the parametrization of Voigt function diverges at sigma = 0. #voigt_broadening #energy_resolution_sigma 0.1 #energy_resolution_gamma 0.01 # This specifies what kind of epsilon we read. # Default is to read epsmat and eps0mat, but if # this flag is present we read file epsdiag.dat instead. # epsdiag.dat contains only the diagonal part of eps(0)mat # which is all that is needed by absorption. It is always created # by an absorption run for use in future runs, to save time reading. #read_epsdiag # Determines output of eigenvectors (eigenvectors) # eig = 0 : do not write eigenvectors (default) # eig < 0 : write all eigenvectors # eig > 0 : write eig eigenvectors #write_eigenvectors eig # Flag the type of kernel to calculate: # spin_triplet: direct kernel only (no exchange). # WARNING: triplet transition matrix elements would be exactly for electric-dipole transitions, # so we give instead the spin part of magnetic-dipole interaction. # spin_singlet (default): direct + exchange. appropriate for spin-polarized too. # local_fields: local-fields + RPA (exchange only) # Note that triplet kernel only applies to a spin-unpolarized system; # for a spin-polarized system, the solutions naturally include both singlets and triplets # (or other multiplicities for a magnetic system). #spin_triplet #spin_singlet #local_fields # Write the bare Coulomb potential V(q+G) to file #write_vcoul # If your two grids are the same, use this flag to skip interpolation and # reduce the time/memory you need. DO NOT use this if you have a different # fine grid from the coarse grid, as for velocity operator. # Then you should use eqp_corrections with eqp.dat (and eqp_q.dat). #skip_interpolation # The new interpolation algorithm is based on the Delaunay tessellation of the # k-points. This guarantees that the interpolant is a continuous function, and # that we are always interpolating, and never extrapolating. (default) #delaunay_interpolation # You can also use the previous interpolation method, which might give # interpolants that are not continuous. #greedy_interpolation # Read from traditional simple binary format for bsedmat/bsexmat instead of HDF5 file format. # Relevant only if code is compiled with HDF5 support. #dont_use_hdf5 # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY (ABSORPTION ONLY) # Average the head of W in addition to the head of V using a model # for the inverse dielectric matrix. This is done for insulators for # all truncation schemes. The W average is limited only to the first # minibz even if cell_average_cutoff != 0. Currently it is always done # regardless whether average_w is included in the input file or not. #average_w # Multiply kernel by arbitrary factor. Default is 1.0 of course. #kernel_scaling 1.0 # Use the same flag as in kernel.inp. #extended_kernel # Solve the full Bethe-Salpeter equation without using the Tamm-Dancoff # approximation. This flag automatically turns on the `extended_kernel` flag. #full_bse # Zero the coupling (H_B) block in the full Bethe-Salpeter equation. This is # useful to test the diagonalization routine. #zero_coupling_block # Perform the co/fi WFN transformation and eqp interpolation without restricting # the character of the coefficients, i.e., write: # |v> = \sum_n d_vn` |n`>, where |n`> is either |v`> or |c`>. # This is a very good idea for metallic systems, but it does not work so well # for semiconductors because of the inherit approximation used in the # interpolation. Notes: # - If extended_kernel is not set, we restrict the d_vn` and d_cn` coefficients # to the subspaces of d_cc` and d_vv` after the eqp interpolation. # - If extended_kernel is set, this flag is automatically turned on, and we # keep the unrestricted d_vn` and d_cn` coefficients for the kernel interpolation. #unrestricted_transformation # Zero out all dvc'/dcv' coefficients. Use this flag together with extended_kernel # to reproduce the result of a restricted kernel calculation. #zero_unrestricted_contribution # The averaging scheme performed for the q=0 term of the BSE Hamiltonian # yields exciton binding energies that do not converge variationally. One # can fix this issue by zeroing out the q=0 term of the interaction, either # before or after the interpolation of the kernel of the BSE. # See Figure 7 of PRB 93, 235435 (2016). # zero_q0_element n # where n is: # 0: don`t zero the W(q=0) term (default) # 1: zero W(q=0) term after interpolation. # 2: zero W(q=0) before interpolation (not recommended) # For 1D and 2D systems, kernel interpolation may not work well if the coarse # k-grid is too coarse to capture fast variations in screening at small q. # The subsample_line flag lets you replace the interpolated matrix elements with # matrix elements from a different (subsampled) bsemat file for |q| < cutoff. # The subsampled bsemat can be calculated on a small patch around each coarse point, # thus allowing for very fine effective k-point sampling. # When this flag is present, during kernel interpolation, a fine k-point, |k_fi>, # is expanded over the closest coarse point, |k_co>, while |k_fi'> is expaned over # over a k-point, |k_sub>, in the subsampled bsemat file s.t. |k_co-k_sub| is as # as close as possible to |k_fi-k_fi'|. The current implementation assumes # that the BSE kernel is isotropic in the voronoi cell around each coarse point. # Use of this flag requires a subsample.inp file in the same directory. # The cutoff is in a.u. #subsample_line cutoff

BSE/inteqp.inp

# inteqp.inp # inteqp.inp uses a subset of the parameters from absorption.inp # Please see absorption.inp for examples.

BSE/README_inteqp

================================================================================ BSE code: Inteqp ================================================================================ Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.0 (July, 2011) J. Deslippe, D. A. Strubbe -------------------------------------------------------------------------------- Description: This code takes the eqp_co.dat file from Sigma and interpolates it from the coarse to the fine grid using wavefunction projections (to resolve band crossings) and linear interpolation in the Brillouin zone. -------------------------------------------------------------------------------- Required Input: inteqp.inp Input parameters. See example absorption.inp in this directory for complete options (noting which sections apply to inteqp). WFN_fi Wavefunctions in unshifted fine grid. WFN_co Wavefunctions on coarse grid. eqp_co.dat A list of quasiparticle energy corrections for the bands in WFN_co. Optional Input: WFNq_fi Wavefunctions in shifted fine grid (used for valence bands if use_velocity is selected) Auxiliary Files: (output files from previous runs - used as input to speed up calculation) dtmat Transformation matrices, dcc/dvv use for interpolation between coarse and fine grid. This file must be consistent with your bsedmat and bsexmat files and corresponding coarse and fine wavefunctions. NOTE: the file format for dtmat was changed in BerkeleyGW 1.1.0 (r5961) -------------------------------------------------------------------------------- Output Files: bandstructure.dat The GW bandstructure on the fine grid. eqp.dat Quasiparticle energy corrections for the bands in WFN_fi. eqp_q.dat Quasiparticle energy corrections for the bands in WFNq_fi (if use_velocity). dvmat_norm.dat The norms of the dvv overlap matrices between the valence band k on the fine grid and the closest k-point on the coarse grid dcmat_norm.dat The norms of the dcc overlap matrices between the conduction band k on the fine grid and the closest k-point on the coarse grid

BSE/summarize_eigenvectors.inp

.true. ! Whether you used TDA. This will usually be .true. 20 ! Number of eigenvectors in file. Set to zero to use default ns*nv*nc*nk 1.5 2.1 ! Emin Emax (eV). Energy window to print information about all states in 3 ! Number of specific states to print A(k). Output files will be exciton_01 ... exciton_99 1.56783332 ! Energy values (eV) of the states to print A(k) 1.67345203 1.96328918

PlotXct

PlotXct/README

================================================================================ PlotXct code ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) Version 0.5 F. Ribeiro (2008), S. Ismail-Beigi Version 0.2 M. L. Tiago (2002-2007) -------------------------------------------------------------------------------- Description: PlotXct plots the exciton wavefunction in real space based on output of BSE/absorption (with full diagonalization). Reads files WFN_fi/WFNq_fi (from mean field) and eigenvectors (output from BSE/absorption code when using diagonalization, not Haydock) and plots selected exciton state in real space according to: Psi(r,r`,s) = Sum_cvk A_svck * phi_sck(r) * exp(ik.r) * conjg( phi_svk(r`) * exp(i[k+q].r`) where r`, hole coordinate, is fixed at some point and r, electron coordinate, runs over a supercell of given size (typically, equivalent to the fine k-grid), with a real-space mesh defined by the FFT grid of the wavefunction files. A separate plot can be generated for each spin s. Output is written in format suitable for Data Explorer (DX). The input option 'restrict_kpoints' reduces the sum over k-points above to a sum over the ones that give most of the contribution to the norm of eigenvectors. This is handy if there are many k-points but only a few of them give sizable contribution. input: WFN_fi WFNq_fi wavefunction files eigenvectors output from BSE/absorption code plotxct.inp input parameters -------------------------------------------------------------------------------- 1. Copy/edit plotxct.inp. You'll need: . index of the exciton state you want to plot . hole position in lattice coordinates . supercell dimensions (or k-grid) . spin component you want to plot (if spin-polarized) 2. Run plotxct.x The ASCII file 'xct.[state]_s[spin].a3Dr' will be created. 'a3Dr' means that the file is in ASCII and contains 3D data in 'r' real space. The header of this file contains information on . state index . state energy in eV . hole position in atomic units (a.u.) . spin component plotted . supercell lattice vectors in a.u. . number of discretization points followed by three columns of data corresponding to the complex values of the electronic part of the excitonic wavefunction, and its magnitude squared. The values are written with very low precision due to file-size concerns. 3. Convert to a format readable by the plotting utility of your choice. Use the 'volume.py' utility: Usage: volume.py imfn imff ivfn ivff ovfn ovff phas cplx [hole] imfn = input matter file name imff = input matter file format (mat|paratec|vasp|espresso|siesta|tbpw|xyz|xsf) ivfn = input volumetric file name ivff = input volumetric file format (a3dr) ovfn = output volumetric file name ovff = output volumetric file format (cube|xsf) phas = remove wavefunction phase (true|false) cplx = complex wavefunction (re|im|abs|abs2) hole = plot hole (true|false) You can specify whether you want a .xsf (XCrysDen) or .cube (Gaussian Cube) file format. You can remove or keep the arbitrary phase of the wavefunction by setting parameter "phas" to true or false. You can plot the re, im, abs, or abs2 part of the wavefunction. You must specify a path to the input file (example: "../01-scf/input") in one of the supported formats (DFT and others) so that the script can obtain the atomic positions from the file. You can choose whether to display or not the position of the hole by setting parameter "hole" to true or false. The resulting .xsf or .cube file can be viewed in XCrysDen or converted to POV-Ray script format using Surface code (for more details on the latter option, see Visual/README). **************** Example: % ~/BerkeleyGW/Visual/volume.py ../01-scf/input paratec xct.000001_s1.a3Dr a3dr \ xct.000001.abs2.xsf xsf false abs2 false % xcrysden --xsf xct.000001.abs2.xsf ****************

PlotXct/plotxct.inp

# # Index of state to be plotted, as it appears in eigenvectors # plot_state 20 # # Index of spin component of the exciton to plot. Default is 1. # plot_spin 1 # # Size of supercell # supercell_size 1 1 60 # # coordinates of the hole in crystal coordinates, in units of supercell lattice vectors # (usually, the hole is near the center of the supercell) # (e.g. center of 1 1 60 supercell should be written as 0.5 0.5 30.0) # hole_position 0.8025 0.3487 30.00 # input option 'restrict_kpoints' reduces the sum over k-points # above to a sum over the specified number that give most of the contribution # to the norm of eigenvectors. This is handy if there are many k-points # but only a few of them give sizable contribution. #restrict_kpoints 5 # q-shift used in the calculation of valence bands (WFNq_fi file) # Only needed if restrict_kpoints is used, otherwise determined automatically. q_shift 0.00000 0.00000 0.00000 # Verbosity level, options are: # 1 = default # 2 = medium - info about k-points, symmetries, and eqp corrections. # 3 = high - full dump of the reduced and unfolded k-points. # 4 = log - log of various function calls. Use to debug code. # 5 = debug - extra debug statements. Use to debug code. # 6 = max - only use if instructed to, severe performance downgrade. # Note that verbosity levels are cumulative. Most users will want to stick # with level 1 and, at most, level 3. Only use level 4+ if debugging the code. #verbosity 1 # EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY # 'unfolded BZ' is from the kpoints in the WFN file # 'full BZ' is generated from the kgrid parameters in the WFN file # See comments in Common/checkbz.f90 for more details # Replace unfolded BZ with full BZ #fullbz_replace # Write unfolded BZ and full BZ to files #fullbz_write

Visual

Visual/README

================================================================================ Visualization tools ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004) -------------------------------------------------------------------------------- Description: This directory contains a set of visualization tools designed to simplify your work with the DFT codes and the BerkeleyGW package. Here you will find the following scripts and codes: 1. Surface is a C++ code for generating an isosurface of a volumetric scalar field (such as the wave function, charge density, or local potential). The scalar field is read from Gaussian Cube or XCrySDen XSF file, the surface triangulation is performed using marching cubes or marching tetrahedra algorithm, and the isosurface is written in the POV-Ray scripting language. The final image is rendered using the ray-tracing program POV-Ray. Running the code requires a fairly complicated input parameter file, described with an example in surface.inp. 2. Matter is a python library for manipulating atomic structures with periodic boundary conditions. It can translate and rotate the atomic coordinates, generate supercells, assemble atomic systems from fragments, and convert between different file formats. The supported file formats are mat, paratec, vasp, espresso, siesta, xyz, xsf, and povray. mat is the native file format of the library. paratec, vasp, espresso, and siesta represent the formats used by different plane-wave and local-orbital DFT codes. xyz is a simple format supported by many molecular viewers, and xsf is the internal format of XCrySDen viewer. povray stands for a scripting language used by the ray-tracing program POV-Ray. The core of the library consists of files common.py, matrix.py, and matter.py. Script convert.py is a command-line driver that performs the basic operations supported by the library. Script link.py is a molecular assembler that can be used to rotate and link two molecules together. Script gsphere.py generates a real-space grid and a sphere of G-vectors given lattice parameters and a kinetic energy cutoff. This helps to estimate the number of unoccupied states needed in GW calculations. Script average.py takes an average of the scalar field on the faces or in the volume of the unit cell. This is used to determine the vacuum level in DFT calculations. Script volume.py converts the a3Dr file produced by PARATEC or BerkeleyGW to Gaussian Cube or XCrySDen XSF format. Each script requires a different set of command-line arguments. Running individual scripts without arguments displays a list of all possible command-line arguments and a short description of each argument. ----------------------------------------------------------------- Examples: 1. Benzene Charge Density This example demonstrates how to plot isosurfaces. Go to directory ./benzene and run ESPRESSO: $ sh link Submit script. Suggested ncpu = 36, walltime = 0:30:00 This will produce the Gaussian Cube file rho.cube containing the charge density of the benzene molecule. For your convenience, the compressed file rho.cube.tgz is included in the ./benzene directory. Let us generate an isosurface that contains 90% of the charge density using the marching cubes algorithm with the smooth triangles and render it in POV-Ray: $ ../surface.x rho_uc.inp $ povray -A0.3 +W640 +H480 +Irho_uc.pov Examine the rho_uc.gif file to find that the pieces of the benzene molecule are placed in the corners of the unit cell. To assemble the pieces together we define a supercell in the rho_sc.inp file. This is done by setting the parameter sc to T and by placing the supercell origin (sco) at position (-0.5 -0.5 -0.5) in crystal coordinates (scu which stands for supercell units is set to latvec). The lattice vectors of the supercell are not changed (scv or supercell vectors in the parameter file). Let us render a new image: $ ../surface.x rho_sc.inp $ povray -A0.3 +W640 +H480 +Irho_sc.pov Now the charge density comes up nice and centered in the middle of the supercell. 2. Nanotube Exciton Wavefunction In this example we will plot an isosurface of the exciton wavefunction. Run ../examples/DFT/swcnt_8-0/ fully. Then go to directory ../examples/DFT/swcnt_8-0/8-absorption/. PlotXct will produce the a3Dr file xct.020_s1.a3Dr containing a wavefunction of the 20th exciton in the (8,0) nanotube. Then volume.py will convert the a3Dr file to Gaussian Cube. $ volume.py ../ESPRESSO/1-scf/in espresso xct.020_s1.a3Dr a3dr xct020.cube cube false abs2 true The command will produce the Gaussian Cube file xct020.cube that contains the squared absolute value of the wavefunction (cplx = abs2) without the sign (phas = false) and the position of the hole (hole = true). Then surface will generate an isosurface that contains 90% of the charge density. $ ../surface.x xct020.inp You can then render it in POV-Ray (which you must install separately): $ povray -A0.3 +W2560 +H1920 +Ixct020.pov The resulting image xct020.gif is included in the example directory. Alternately, you can visualize the Cube file directly in XCrySDen. 3. Rock-Salt Lattice Here you will learn how to make large supercells of bulk crystals. Go to directory ./rocksalt where you will find the nacl.mat file. Render it in POV-Ray: $ ../convert.py nacl.mat mat nacl.pov povray $ povray -A0.3 +W640 +H480 +Inacl.pov The unit cell contains only two atoms. Let us make a supercell that contains a fractional number of unit cells. The supercell is described by the sc1 file which defines the origin of the supercell, the lattice vectors of the supercell, and the units in which these quantities are given. These are equivalent to sco, scv, and scu in the surface parameter file in the first example. The last line in the sc1 file corresponds to sct (supercell translation) in the surface parameter file. We will get back to it later on. Let us render the supercell: $ ../convert.py nacl.mat mat nacl_sc1.pov povray supercell sc1 $ povray -A0.3 +W640 +H480 +Inacl_sc1.pov Note the broken bonds on the faces of the supercell. That is because the supercell contains a fractional number of the unit cells, so the translational symmetry is broken which results in the Na-Na and Cl-Cl bonds. We disable the translational symmetry of the supercell by setting sct to false (the last line in the sc2 file). This enforces the translational symmetry of the underlying unit cell structure. Render the new supercell in POV-Ray: $ ../convert.py nacl.mat mat nacl_sc2.pov povray supercell sc2 $ povray -A0.3 +W640 +H480 +Inacl_sc2.pov Now the bonds on the faces of the supercell come out right. 4. Organic Molecule Synthesis In this example you will assemble the bipolar molecule, bithiophene naphthalene diimide, from the donor and acceptor units, bithiophene and naphthalene diimide. Go to directory ./btnd and open files nd.xyz and bt.xyz in any molecular viewer, for example Jmol. Identify the atoms you want to link together, these are the two carbon atoms, # 15 in nd.xyz and # 8 in bt.xyz. You need to remove the two hydrogen atoms, # 21 in nd.xyz and # 14 in bt.xyz, and place # 15 and # 8 at the distance of 1.49 Angstrom from each other along the 15-21-14-8 line. This is done by invoking the following command: $ ../link.py nd.xyz xyz bt.xyz xyz btnd.xyz xyz 15 21 8 14 0.0 degree 1.49 angstrom You can also rotate bt.xyz around the 15-21-14-8 axis by an arbitrary angle, although the rotation angle is set to zero in the above command. 5. Estimate the number of unoccupied states for Epsilon and Sigma Go to directory ../examples/DFT/benzene/0-gsphere/ and run the following: $ gsphere.py g_eps.in g_eps.out Examine input file g_eps.in. It contains the lattice vectors in bohr, the cutoff energy in Ry (epsilon_cutoff from ../5-gw/epsilon.inp or screened_coulomb_cutoff from ../5-gw/sigma.inp), '0 0 0' for the FFT grid to be determined automatically, and 'true' to sort the G-vectors by their kinetic energies. Examine output file g_eps.out. Look for the number of G-vectors, ng. You will find 'ng = 2637' meaning that you will need at least that many unoccupied states. Of course the number of unoccupied states is a convergence parameter, but gsphere.py gives you an idea in which range of values should you check the convergence. Now run the following: $ gsphere.py g_rho.in g_rho.out Input file g_rho.in is similar to g_eps.in but it has a different cutoff energy which is 4 times ecutwfc from ../ESPRESSO/1-scf/in. This is the charge density cutoff or ecutrho in espresso documentation. Note that the last line in g_rho.in is set to 'false'. This is because using built-in Python sort function on that many G-vectors (up to ecutrho) will freeze your python interpreter. Examine output file g_rho.out. You should see the following: grid = ( 128 72 140 ) -- minimal ( 128 72 140 ) -- factors 2, 3, 5, 7, 1*11, 1*13 ( 128 72 144 ) -- factors 2, 3, 5 The third line is the size of FFT grid in espresso calculation. (Well, not necessarily, because espresso algorithm starting with version 5 is smarter than what is implemented in gsphere.py.) The z-component is equal to 144 meaning that for an optimal load-balancing you should run espresso on a number of cores which is a divisor of 144 (that is, 144, 72, 36, 18, etc. cores). ----------------------------------------------------------------- Notes: Matter library may lack support for some advanced features of PARATEC, VASP, ESPRESSO and SIESTA formats. For example, LatticeParameters and ZMatrix are not implemented for SIESTA. This can be added to functions paratec_read, paratec_write, vasp_read, vasp_write, espresso_read, espresso_write, siesta_read and siesta_write in file matter.py. Also note that all the additional information not related to the crystal structure (k-points, energy cutoffs, etc.) will be lost and replaced with the default parameters when converting between PARATEC, VASP, ESPRESSO and SIESTA formats.

Visual/surface.inp

parameter file | example (HOMO of benzene) -------------------------------------------------------------------------------- header text | header C6H6_band_15 inputfilename file | inputfilename C6H6.b_15.cube inputfileformat cube|xsf | inputfileformat cube outputfilename file | outputfilename C6H6.b_15.pov outputfileformat povray | outputfileformat povray isovalue (0.0,1.0) | isovalue 0.9 sign positive|negative|both | sign both power 0|1|2 | power 1 algorithm cube|tetrahedron | algorithm cube smooth T|F | smooth T box T|F | box F basis T|F | basis F uc T|F | uc F uco | uco ucox ucoy ucoz | 0.0 0.0 0.0 ucv | ucv ucv1x ucv1y ucv1z | 1.0 0.0 0.0 ucv2x ucv2y ucv2z | 0.0 1.0 0.0 ucv3x ucv3y ucv3z | 0.0 0.0 1.0 ucu bohr|angstrom|latvec | ucu latvec sc T|F | sc T sco | sco scox scoy scoz | -0.5 -0.5 -0.5 scv | scv scv1x scv1y scv1z | 1.0 0.0 0.0 scv2x scv2y scv2z | 0.0 1.0 0.0 scv3x scv3y scv3z | 0.0 0.0 1.0 scu bohr|angstrom|latvec | scu latvec sct T|F | sct T -------------------------------------------------------------------------------- the isosurface is defined by isovalue * max |psi| for power = 0 and by integral_v |psi|^power = isovalue * integral |psi|^power for power > 0 where psi is the scalar field and v is the volume inside the isosurface note that espresso already outputs |psi|^2, setting power = 2 yields |psi|^4 in this case, to produce |psi|^2 isosurface set power = 1 algorithm stands for marching cubes and marching tetrahedra smooth defines whether to average normals for smooth rendering box specifies whether to generate supercell box in povray script basis specifies whether to generate coordinate axes in povray script sfo = scalar field origin sfv = scalar field vectors uco = unit cell origin ucv = unit cell vectors ucu = unit cell units sco = supercell origin scv = supercell vectors scu = supercell units sct = supercell translational symmetry sfo/sfv are read from volumetric file if uc = T then uco/ucv are read from parameter file else uco/ucv are set to sfo/sfv if sc = T then sco/scv are read from parameter file else sco/scv are set to uco/ucv if uc = T and ucu = latvec then uco/ucv are scaled by sfv if sc = T and scu = latvec then sco/scv are scaled by ucv if sct = T then scv is used for translational symmetry else ucv is used for translational symmetry in most cases, set uc = F (uc = T is only needed if volumetric data do not span the whole unit cell and the supercell is being used, so the correct unit cell must be defined) use sc = T to construct the supercell spanning several unit cells or to assemble the unit cell around the origin of the coordinate system as in benzene example above (sco = (-0.5 -0.5 -0.5) in latvec units) the supercell may span a fractional number of unit cells, in this case set sct = F to produce the correct bonds at the faces of the supercell

Visual/gsphere.inp

25.917768986 0.000000000 0.000000000 0.000000000 14.496126116 0.000000000 0.000000000 0.000000000 28.284379996 240.0 0 0 0 false 0.0 0.0 0.0 # example input file for gsphere.py, for benzene # a1x a1y a1z [= lattice vectors (bohr)] # a2x a2y a2z # a3x a3y a3z # energy cutoff (Ry) # FFT_grid_x FFT_grid_y FFT_grid_z (set to zero to determine automatically) # whether to sort G-vectors by kinetic energy (true) or leave unsorted (false) # kx ky kz (k-point at which to generate G-vectors, crystal coordinates)

Developers

doxygen/README

================================================================================ BerkeleyGW Doxygen documentation ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. Version 1.1 (June, 2014) Version 1.0 (July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze Version 0.5 J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008) Version 0.2 M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004) -------------------------------------------------------------------------------- Description ----------- This directory automatically generates documentation for BerkeleyGW using Doxygen. This is aimed towards developers, and end-users might as well just ignore this directory. To create the documentation, simply type `make`. You`ll need doxygen and graphviz installed. Then open doxygen/html/index.html in a web browser. Obtaining Doxygen and Graphviz ------------------------------ Doxygen and graphviz are available at: http://www.doxygen.org/ http://www.graphviz.org/ Alternatively, if you have a Debian-based distribution, such as Ubuntu, you can ask your administrator to install the following packages: apt-get install doxygen graphviz or on MacOS with MacPorts (www.macports.org): port install doxygen graphviz

Common/README

================================================================================ BerkeleyGW: Common directory (developer info) ================================================================================ Version 2.0 (May, 2018) To be announced. Version 1.2 (Aug, 2016) F. H. da Jornada, J. Deslippe, D. Vigil-Fowler, J. I. Mustafa, T. Rangel, F. Bruneval, F. Liu, D. Y. Qiu, D. A. Strubbe, G. Samsonidze, J. Lischner. -------------------------------------------------------------------------------- Description: This directory contains common files shared by different components of the BerkeleyGW package. The most important files are described below: 1. typedefs.f90 This file contains the derived data types that are used throughout the code. 2. nrtype.f90 This file contains some general constants and the definitions of single- and double-precision real and complex types following the convention of the Numerical Recipes book. The definitions of DP and DPC are used throughout the code. It also contains the fundamental physical constants. The units used throughout the code are Rydberg atomic units with a few exceptions, such as eV in Sigma and Hartree atomic units in EPM. The difference between Hartree and Rydberg atomic units is sketched below. Hartree atomic units: hbar=1 e=1 m=1 a0=hbar^2/(m*e^2)=1 E=hbar^2/(2*m*a0^2)=0.5 Rydberg atomic units: hbar=1 e=sqrt(2) m=0.5 a0=hbar^2/(m*e^2)=1 E=hbar^2/(2*m*a0^2)=1 3. f_defs.h This file contains preprocessor definitions for the built-in Fortran functions. This helps to avoid accidental conversion from double to single precision.

Common/qhull/README

DISCLAIMER ========== This directory contains source code from Qhull. The file COPYING.txt has the terms for distributing these files. The following files are part of the BerkeleyGW package, and not Qhull: - libtile_qhull.c - libtile_qhull.h - test_delaunay_f.f90 - test_delaunay_c.c - Makefile - README The files listed above are distributed under the BerkeleyGW license found in the topmost directory. CHANGES TO QHULL ================ The following change had to be made to Qhull: - qhull_a.h: line 105 Remove macro for intel compilers. Source: http://mail.scipy.org/pipermail/scipy-user/2011-July/029908.html

MeanField/spglib-1.0.9/README

* Imported spglib-1.0.9 from http://spglib.sourceforge.net. This is a BSD-licensed C library for symmetries by Atsushi Togo. --DAS * Added src/spglib_f.c which is not actually part of spglib 1.0.9 although it appears to have been forgotten by accident since it is mentioned in the documentation and was present in earlier version. I obtained it by e-mailing the author. --DAS * Removed test directory which we do not need and contains a large number of files. --DAS * Removed examples, python, etc., blank files, and automake/libtool-related files. --DAS 

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