diff --git a/.doctrees/citation.doctree b/.doctrees/citation.doctree index 2432743b..6e8406c5 100644 Binary files a/.doctrees/citation.doctree and b/.doctrees/citation.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 1a3b6ca3..f8448636 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/_sources/citation.md b/_sources/citation.md index 9df0a8d7..6c7eb171 100644 --- a/_sources/citation.md +++ b/_sources/citation.md @@ -24,26 +24,27 @@ indeed helps the phono3py project to continue: } ``` -- "First-principles Phonon Calculations with Phonopy and Phono3py", +- "Implementation strategies in phonopy and phono3py", - Atsushi Togo, J. Phys. Soc. Jpn., **92**, 012001-1-21 (2023) + Atsushi Togo, Laurent Chaput, Terumasa Tadano, and Isao Tanaka, J. Phys. Condens. Matter **35**, 353001-1-22 (2023) - https://doi.org/10.7566/JPSJ.92.012001 (Open access) + https://dx.doi.org/10.1088/1361-648X/acd831 (Open access) ``` - @article{phonopy-phono3py-JPSJ, - author = {Togo ,Atsushi}, - title = {First-principles Phonon Calculations with Phonopy and Phono3py}, - journal = {J. Phys. Soc. Jpn.}, - volume = {92}, - number = {1}, - pages = {012001}, + @article{phonopy-phono3py-JPCM, + author = {Togo, Atsushi and Chaput, Laurent and Tadano, Terumasa and Tanaka, Isao}, + title = {Implementation strategies in phonopy and phono3py}, + journal = {J. Phys. Condens. Matter}, + volume = {35}, + number = {35}, + pages = {353001}, year = {2023}, - doi = {10.7566/JPSJ.92.012001} + doi = {10.1088/1361-648X/acd831} } ``` (citation_direct_solution_lbte)= + ## Citation of direct solution of LBTE (`--lbte`) If you have used direct solution of LBTE in phono3py, please cite the @@ -75,8 +76,9 @@ If you have used the solution of the Wigner transport equation in phono3py, plea following articles: (citation_unified_theory)= + - "Unified theory of thermal transport in crystals and glasses" - Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Nat. Phys., **15**, 809 (2019) + Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Nat. Phys., **15**, 809 (2019) ``` @article{NatPhys.15.809, @@ -92,9 +94,11 @@ following articles: url = {https://www.nature.com/articles/s41567-019-0520-x} } ``` -(citation_wigner_formulation)= + + (citation_wigner_formulation)= + - "Wigner formulation of thermal transport in solids" - Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Physical Review X **12**, 041011 (2022) + Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Physical Review X **12**, 041011 (2022) ``` @article{PhysRevX.12.041011, diff --git a/citation.html b/citation.html index 250f0302..43bf8ed4 100644 --- a/citation.html +++ b/citation.html @@ -342,18 +342,18 @@

Citation of phono3py -

  • “First-principles Phonon Calculations with Phonopy and Phono3py”,

    -

    Atsushi Togo, J. Phys. Soc. Jpn., 92, 012001-1-21 (2023)

    -

    https://doi.org/10.7566/JPSJ.92.012001 (Open access)

    -
    @article{phonopy-phono3py-JPSJ,
-  author  = {Togo ,Atsushi},
-  title   = {First-principles Phonon Calculations with Phonopy and Phono3py},
-  journal = {J. Phys. Soc. Jpn.},
-  volume  = {92},
-  number  = {1},
-  pages   = {012001},
+
  • “Implementation strategies in phonopy and phono3py”,
    
+
    Atsushi Togo, Laurent Chaput, Terumasa Tadano, and Isao Tanaka, J. Phys. Condens. Matter 35, 353001-1-22 (2023)
    
+
    https://dx.doi.org/10.1088/1361-648X/acd831 (Open access)
    
+
    @article{phonopy-phono3py-JPCM,
+  author  = {Togo, Atsushi and Chaput, Laurent and Tadano, Terumasa and Tanaka, Isao},
+  title   = {Implementation strategies in phonopy and phono3py},
+  journal = {J. Phys. Condens. Matter},
+  volume  = {35},
+  number  = {35},
+  pages   = {353001},
   year    = {2023},
-  doi     = {10.7566/JPSJ.92.012001}
+  doi     = {10.1088/1361-648X/acd831}
 }
 
    
 
    
@@ -392,7 +392,7 @@ 
    Citation of solution of the Wigner transport equation (
 
  • “Unified theory of thermal transport in crystals and glasses”
-Michele Simoncelli, Nicola  Marzari, and Francesco Mauri, Nat. Phys., 15, 809 (2019)
    
+Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Nat. Phys., 15, 809 (2019)
    
 
    @article{NatPhys.15.809,
   title={Unified theory of thermal transport in crystals and glasses},
   author={Simoncelli, Michele and Marzari, Nicola and Mauri, Francesco},
@@ -408,10 +408,8 @@ 
    Citation of solution of the Wigner transport equation (
-
  • “Wigner formulation of thermal transport in solids”
-Michele Simoncelli, Nicola  Marzari, and Francesco Mauri, Physical Review X 12, 041011 (2022)
    
+
  • “Wigner formulation of thermal transport in solids”
+Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Physical Review X 12, 041011 (2022)
    
 
    @article{PhysRevX.12.041011,
   title = {Wigner Formulation of Thermal Transport in Solids},
   author = {Simoncelli, Michele and Marzari, Nicola and Mauri, Francesco},
diff --git a/searchindex.js b/searchindex.js
index 7f1971a2..2629f78e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"xmax-and-ymax"]], "--zmax": [[1, "zmax"]], "--dr, --density-ratio": [[1, "dr-density-ratio"]], "--cmap": [[1, "cmap"]], "Change Log": [[2, "change-log"]], "Jul-3-2023: Version 2.7.0": [[2, "jul-3-2023-version-2-7-0"]], "Apr-3-2023: Version 2.6.0": [[2, "apr-3-2023-version-2-6-0"]], "Dec-31-2022: Version 2.5.1": [[2, "dec-31-2022-version-2-5-1"]], "Dec-29-2022: Version 2.5.0": [[2, "dec-29-2022-version-2-5-0"]], "Oct-6-2022: Version 2.4.1": [[2, "oct-6-2022-version-2-4-1"]], "Oct-5-2022: Version 2.4.0": [[2, "oct-5-2022-version-2-4-0"]], "May-28-2022: Version 2.3.2": [[2, "may-28-2022-version-2-3-2"]], "May-7-2022: Version 2.3.1": [[2, "may-7-2022-version-2-3-1"]], "Apr-9-2022: Version 2.3.0": [[2, "apr-9-2022-version-2-3-0"]], "Feb-14-2022: Version 2.2.0": [[2, "feb-14-2022-version-2-2-0"]], "Nov-3-2021: Version 2.1.0": [[2, "nov-3-2021-version-2-1-0"]], "Jul-22-2021: Version 2.0.0": [[2, "jul-22-2021-version-2-0-0"]], "Mar-17-2021: Version 1.22.3": [[2, "mar-17-2021-version-1-22-3"]], "Feb-21-2021: Version 1.22.2": [[2, "feb-21-2021-version-1-22-2"]], "Feb-21-2021: Version 1.22.1": [[2, "feb-21-2021-version-1-22-1"]], "Jan-29-2021: Version 1.22.0": [[2, "jan-29-2021-version-1-22-0"]], "Sep-30-2020: Version 1.21.0": [[2, "sep-30-2020-version-1-21-0"]], "Mar-3-2020: Version 1.20.0": [[2, "mar-3-2020-version-1-20-0"]], "Mar-3-2020: Version 1.19.1": [[2, "mar-3-2020-version-1-19-1"]], "Mar-2-2020: Version 1.19.0": [[2, "mar-2-2020-version-1-19-0"]], "Dec-22-2019: Version 1.18.2": [[2, "dec-22-2019-version-1-18-2"]], "Oct-17-2019: Version 1.18.1": [[2, "oct-17-2019-version-1-18-1"]], "Oct-9-2019: Version 1.18.0": [[2, "oct-9-2019-version-1-18-0"]], "Apr-18-2019: Version 1.17.0": [[2, "apr-18-2019-version-1-17-0"]], "Mar-24-2019: Version 1.16.0": [[2, "mar-24-2019-version-1-16-0"]], "Nov-22-2018: version 1.14.3": [[2, "nov-22-2018-version-1-14-3"]], "June-20-2018: version 1.13.3": [[2, "june-20-2018-version-1-13-3"]], "May-17-2018: version 1.13.1": [[2, "may-17-2018-version-1-13-1"]], "Mar-16-2018: version 1.12.9": [[2, "mar-16-2018-version-1-12-9"]], "Feb-1-2018: version 1.12.7": [[2, "feb-1-2018-version-1-12-7"]], "Nov-22-2017: version 1.12.5": [[2, "nov-22-2017-version-1-12-5"]], "Nov-17-2017: version 1.12.3": [[2, "nov-17-2017-version-1-12-3"]], "Jun-18-2017: version 1.11.13": [[2, "jun-18-2017-version-1-11-13"]], "Mar-31-2017: version 1.11.11": [[2, "mar-31-2017-version-1-11-11"]], "Feb-9-2017: version 1.11.9": [[2, "feb-9-2017-version-1-11-9"]], "Dec-14-2016: version 1.11.7": [[2, "dec-14-2016-version-1-11-7"]], "Nov-27-2016: version 1.11.5": [[2, "nov-27-2016-version-1-11-5"]], "Apr-24-2016: version 1.10.9": [[2, "apr-24-2016-version-1-10-9"]], "Apr-16-2016: version 1.10.7": [[2, "apr-16-2016-version-1-10-7"]], "Mar-15-2016: version 1.10.5": [[2, "mar-15-2016-version-1-10-5"]], "Oct-10-2015: version 0.9.14": [[2, "oct-10-2015-version-0-9-14"]], "Sep-26-2015: version 0.9.13": [[2, "sep-26-2015-version-0-9-13"]], "Aug-12-2015: version 0.9.12": [[2, "aug-12-2015-version-0-9-12"]], "Jun-18-2015: version 0.9.10.1": [[2, "jun-18-2015-version-0-9-10-1"]], "Jun-17-2015: version 0.9.10": [[2, "jun-17-2015-version-0-9-10"]], "Changes in version 0.9.7": [[2, "changes-in-version-0-9-7"]], "Changes in version 0.9.6": [[2, "changes-in-version-0-9-6"]], "Changes in version 0.9.5": [[2, "changes-in-version-0-9-5"]], "Changes in version 0.9.4": [[2, "changes-in-version-0-9-4"]], "Changes in version 0.8.11": [[2, "changes-in-version-0-8-11"]], "Changes in version 0.8.10": [[2, "changes-in-version-0-8-10"]], "Changes in version 0.8.2": [[2, "changes-in-version-0-8-2"]], "Changes in version 0.8.0": [[2, "changes-in-version-0-8-0"]], "Changes in version 0.7.6": [[2, "changes-in-version-0-7-6"]], "Changes in version 0.7.2": [[2, "changes-in-version-0-7-2"]], "Changes in version 0.7.1": [[2, "changes-in-version-0-7-1"]], "Changes in version 0.6.0": [[2, "changes-in-version-0-6-0"]], "How to cite phono3py": [[3, "how-to-cite-phono3py"]], "Citation of phono3py": [[3, "citation-of-phono3py"]], "Citation of direct solution of LBTE (--lbte)": [[3, "citation-of-direct-solution-of-lbte-lbte"]], "Citation of solution of the Wigner transport equation (--wigner)": [[3, "citation-of-solution-of-the-wigner-transport-equation-wigner"]], "Command options / Setting tags": [[4, "command-options-setting-tags"]], "Input cell file name": [[4, "input-cell-file-name"]], "-c (CELL_FILENAME)": [[4, "c-cell-filename"]], "Calculator interface": [[4, "calculator-interface"]], "--qe (CALCULATOR = QE)": [[4, "qe-calculator-qe"]], "--crystal (CALCULATOR = CRYSTAL)": [[4, "crystal-calculator-crystal"]], "--turbomole (CALCULATOR = TURBOMOLE)": [[4, "turbomole-calculator-turbomole"]], "Utilities to create default input files": [[4, "utilities-to-create-default-input-files"]], "--cf3 (command option only)": [[4, "cf3-command-option-only"]], "--cf3-file (command option only)": [[4, "cf3-file-command-option-only"]], "--cf2 (command option only)": [[4, "cf2-command-option-only"]], "--cfz (command option only)": [[4, "cfz-command-option-only"]], "--fs2f2 or --force-sets-to-forces-fc2 (command option only)": [[4, "fs2f2-or-force-sets-to-forces-fc2-command-option-only"]], "--cfs or --create-force-sets (command option only)": [[4, "cfs-or-create-force-sets-command-option-only"]], "Supercell, primitive cell, masses, magnetic moments": [[4, "supercell-primitive-cell-masses-magnetic-moments"]], "--dim (DIM)": [[4, "dim-dim"]], "--dim-fc2 (DIM_FC2)": [[4, "dim-fc2-dim-fc2"]], "--pa, --primitive-axes (PRIMITIVE_AXES)": [[4, "pa-primitive-axes-primitive-axes"]], "--mass (MASS)": [[4, "mass-mass"]], "--magmom (MAGMOM)": [[4, "magmom-magmom"]], "Displacement creation": [[4, "displacement-creation"]], "-d (CREATE_DISPLACEMENTS = .TRUE.)": [[4, "d-create-displacements-true"]], "--amplitude (DISPLACEMENT_DISTANCE)": [[4, "amplitude-displacement-distance"]], "Force constants": [[4, "force-constants"]], "--cfc or --compact-fc (COMPACT_FC = .TRUE.)": [[4, "cfc-or-compact-fc-compact-fc-true"]], "--sym-fc (FC_SYMMETRY = .TRUE.)": [[4, "sym-fc-fc-symmetry-true"]], "--cutoff-fc3 or --cutoff-fc3-distance (CUTOFF_FC3_DISTANCE)": [[4, "cutoff-fc3-or-cutoff-fc3-distance-cutoff-fc3-distance"]], "--cutoff-pair or --cutoff-pair-distance (CUTOFF_PAIR_DISTANCE)": [[4, "cutoff-pair-or-cutoff-pair-distance-cutoff-pair-distance"]], "--alm": [[4, "alm"]], "Reciprocal space sampling mesh and grid points, and band indices": [[4, "reciprocal-space-sampling-mesh-and-grid-points-and-band-indices"]], "--mesh (MESH or MESH_NUMBERS)": [[4, "mesh-mesh-or-mesh-numbers"]], "--gp (GRID_POINTS)": [[4, "gp-grid-points"]], "--ga (GRID_ADDRESSES)": [[4, "ga-grid-addresses"]], "--bi (BAND_INDICES)": [[4, "bi-band-indices"]], "--wgp (command option only)": [[4, "wgp-command-option-only"]], "--stp (command option only)": [[4, "stp-command-option-only"]], "Brillouin zone integration": [[4, "brillouin-zone-integration"]], "--thm (TETRAHEDRON = .TRUE.)": [[4, "thm-tetrahedron-true"]], "--sigma (SIGMA)": [[4, "sigma-sigma"]], "--sigma-cutoff (SIGMA_CUTOFF_WIDTH)": [[4, "sigma-cutoff-sigma-cutoff-width"]], "--full-pp (FULL_PP = .TRUE.)": [[4, "full-pp-full-pp-true"]], "Methods to solve phonon Boltzmann equation and Wigner formulation": [[4, "methods-to-solve-phonon-boltzmann-equation-and-wigner-formulation"]], "--br (BTERTA = .TRUE.)": [[4, "br-bterta-true"]], "--lbte (LBTE = .TRUE.)": [[4, "lbte-lbte-true"]], "--wigner": [[4, "wigner"]], "Scattering": [[4, "scattering"]], "--isotope (ISOTOPE =.TRUE.)": [[4, "isotope-isotope-true"]], "--mass-variances or --mv (MASS_VARIANCES)": [[4, "mass-variances-or-mv-mass-variances"]], "--boundary-mfp, --bmfp (BOUNDARY_MFP)": [[4, "boundary-mfp-bmfp-boundary-mfp"]], "--ave-pp (USE_AVE_PP = .TRUE.)": [[4, "ave-pp-use-ave-pp-true"]], "--const-ave-pp (CONST_AVE_PP = .TRUE.)": [[4, "const-ave-pp-const-ave-pp-true"]], "--nu (N_U = .TRUE.)": [[4, "nu-n-u-true"]], "--scattering-event-class (SCATTERING_EVENT_CLASS)": [[4, "scattering-event-class-scattering-event-class"]], "Temperature": [[4, "temperature"]], "--ts (TEMPERATURES): Temperatures": [[4, "ts-temperatures-temperatures"]], "--tmax, --tmin, --tstep (TMAX, TMIN, TSTEP)": [[4, "tmax-tmin-tstep-tmax-tmin-tstep"]], "Non-analytical term correction": [[4, "non-analytical-term-correction"]], "--nac (NAC = .TRUE.)": [[4, "nac-nac-true"]], "--q-direction (Q_DIRECTION)": [[4, "q-direction-q-direction"]], "Imaginary and real parts of self energy": [[4, "imaginary-and-real-parts-of-self-energy"]], "--ise (IMAG_SELF_ENERGY = .TRUE.)": [[4, "ise-imag-self-energy-true"]], "--rse (REAL_SELF_ENERGY = .TRUE.)": [[4, "rse-real-self-energy-true"]], "Spectral function": [[4, "spectral-function"]], "--spf (SPECTRAL_FUNCTION = .TRUE.)": [[4, "spf-spectral-function-true"]], "Joint density of states (JDOS) and weighted-JDOS": [[4, "joint-density-of-states-jdos-and-weighted-jdos"]], "--jdos (JOINT_DOS = .TRUE.)": [[4, "jdos-joint-dos-true"]], "Sampling frequency for distribution functions": [[4, "sampling-frequency-for-distribution-functions"]], "--num-freq-points, --freq-pitch (NUM_FREQUENCY_POINTS)": [[4, "num-freq-points-freq-pitch-num-frequency-points"]], "Mode-Gruneisen parameter from 3rd order force constants": [[4, "mode-gruneisen-parameter-from-3rd-order-force-constants"]], "--gruneisen (GRUNEISEN = .TRUE.)": [[4, "gruneisen-gruneisen-true"]], "File I/O": [[4, "file-i-o"]], "--fc2 (READ_FC2 = .TRUE.)": [[4, "fc2-read-fc2-true"]], "--fc3 (READ_FC3 = .TRUE.)": [[4, "fc3-read-fc3-true"]], "--write-gamma (WRITE_GAMMA = .TRUE.)": [[4, "write-gamma-write-gamma-true"]], "--read-gamma (READ_GAMMA = .TRUE.)": [[4, "read-gamma-read-gamma-true"]], "--write-gamma-detail (WRITE_GAMMA_DETAIL = .TRUE.)": [[4, "write-gamma-detail-write-gamma-detail-true"]], "--write-phonon (WRITE_PHONON = .TRUE.)": [[4, "write-phonon-write-phonon-true"]], "--read-phonon (READ_PHONON = .TRUE.)": [[4, "read-phonon-read-phonon-true"]], "--write-pp (WRITE_PP = .TRUE.) and --read-pp (READ_PP = .TRUE.)": [[4, "write-pp-write-pp-true-and-read-pp-read-pp-true"]], "--hdf5-compression (command option only)": [[4, "hdf5-compression-command-option-only"]], "-o (command option only)": [[4, "o-command-option-only"]], "-i (command option only)": [[4, "i-command-option-only"]], "--io (command option only)": [[4, "io-command-option-only"]], "CRYSTAL & phono3py calculation": [[5, "crystal-phono3py-calculation"]], "Workflow": [[5, "workflow"], [17, "workflow"], [20, "workflow"], [21, "workflow"], [23, "workflow"]], "Force constants calculation with cutoff pair-distance": [[6, "force-constants-calculation-with-cutoff-pair-distance"]], "What is cutff pair-distance in phono3py?": [[6, "what-is-cutff-pair-distance-in-phono3py"]], "Usage": [[6, "usage"]], "Creating supercells with displacements": [[6, "creating-supercells-with-displacements"]], "Supercell files": [[6, "supercell-files"]], "Special phono3py_disp.yaml": [[6, "special-phono3py-disp-yaml"]], "Making FORCES_FC3": [[6, "making-forces-fc3"]], "Running phonon-phonon interaction calculation": [[6, "running-phonon-phonon-interaction-calculation"]], "A script extract supercell IDs from phono3py_disp.yaml": [[6, "a-script-extract-supercell-ids-from-phono3py-disp-yaml"]], "Tests": [[6, "tests"]], "Si-PBE": [[6, "si-pbe"]], "AlN-LDA": [[6, "aln-lda"]], "Direct solution of linearized phonon Boltzmann equation": [[7, "direct-solution-of-linearized-phonon-boltzmann-equation"]], "How to use": [[7, "how-to-use"], [22, "how-to-use"]], "Memory usage": [[7, "memory-usage"]], "Work load distribution": [[7, "work-load-distribution"]], "Distribution of collision matrix": [[7, "distribution-of-collision-matrix"]], "Distribution of phonon-phonon interaction strengths": [[7, "distribution-of-phonon-phonon-interaction-strengths"]], "Cutoff parameter of pseudo inversion": [[7, "cutoff-parameter-of-pseudo-inversion"]], "Diagonalization solver interfaces": [[7, "diagonalization-solver-interfaces"]], "OpenBLAS or MKL linked scipy and numpy": [[7, "openblas-or-mkl-linked-scipy-and-numpy"]], "OpenBLAS or MKL via LAPACKE": [[7, "openblas-or-mkl-via-lapacke"]], "Solver choice for diagonalization": [[7, "solver-choice-for-diagonalization"]], "Examples": [[8, "examples"]], "External tools": [[9, "external-tools"]], "Phono3py-Power-Tools": [[9, "phono3py-power-tools"]], "Kinetic Collective Model": [[9, "kinetic-collective-model"]], "How to read the results stored in hdf5 files": [[10, "how-to-read-the-results-stored-in-hdf5-files"]], "How to use HDF5 python library": [[10, "how-to-use-hdf5-python-library"]], "Details of kappa-*.hdf5 file": [[10, "details-of-kappa-hdf5-file"]], "mesh": [[10, "mesh"]], "frequency": [[10, "frequency"]], "gamma": [[10, "gamma"]], "gamma_isotope": [[10, "gamma-isotope"]], "group_velocity": [[10, "group-velocity"]], "heat_capacity": [[10, "heat-capacity"]], "kappa": [[10, "kappa"]], "mode-kappa": [[10, "mode-kappa"]], "gv_by_gv": [[10, "gv-by-gv"]], "q-point": [[10, "q-point"]], "temperature": [[10, "temperature"]], "weight": [[10, "weight"]], "ave_pp": [[10, "ave-pp"]], "kappa_unit_conversion": [[10, "kappa-unit-conversion"]], "How to know grid point index number corresponding to grid address": [[10, "how-to-know-grid-point-index-number-corresponding-to-grid-address"]], "Welcome to phono3py": [[11, "welcome-to-phono3py"]], "Documentation": [[11, "documentation"]], "Mailing list": [[11, "mailing-list"]], "License": [[11, "license"]], "Contact": [[11, "contact"]], "Input / Output files": [[12, "input-output-files"]], "Intermediate text files": [[12, "intermediate-text-files"]], "phono3py_disp.yaml": [[12, "phono3py-disp-yaml"]], "FORCES_FC3": [[12, "forces-fc3"]], "FORCES_FC2": [[12, "forces-fc2"]], "HDF5 files": [[12, "hdf5-files"]], "kappa-*.hdf5": [[12, "kappa-hdf5"]], "fc3.hdf5": [[12, "fc3-hdf5"]], "fc2.hdf5": [[12, "fc2-hdf5"]], "gamma-*.hdf5": [[12, "gamma-hdf5"]], "gamma_detail-*.hdf5": [[12, "gamma-detail-hdf5"]], "Simple text file": [[12, "simple-text-file"]], "gammas-*.dat": [[12, "gammas-dat"]], "jdos-*.dat": [[12, "jdos-dat"]], "linewidth-*.dat": [[12, "linewidth-dat"]], "Installation": [[13, "installation"]], "Installation using conda": [[13, "installation-using-conda"]], "Installation from source code": [[13, "installation-from-source-code"]], "Build with automatic search of library configurations by cmake": [[13, "build-with-automatic-search-of-library-configurations-by-cmake"]], "Build with custom library configurations by site.cfg file": [[13, "build-with-custom-library-configurations-by-site-cfg-file"]], "Installation instruction of latest development version of phono3py": [[13, "installation-instruction-of-latest-development-version-of-phono3py"]], "Installation of LAPACKE": [[13, "installation-of-lapacke"]], "OpenBLAS provided by conda": [[13, "openblas-provided-by-conda"]], "Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS)": [[13, "netlib-lapacke-provided-by-ubuntu-package-manager-with-single-thread-blas"]], "Compiling Netlib LAPACKE": [[13, "compiling-netlib-lapacke"]], "Multithreading and its controlling by C macro": [[13, "multithreading-and-its-controlling-by-c-macro"]], "OpenMP library of gcc": [[13, "openmp-library-of-gcc"]], "Trouble shooting": [[13, "trouble-shooting"]], "Interfaces to calculators": [[14, "interfaces-to-calculators"]], "Calculator specific behaviors": [[14, "calculator-specific-behaviors"]], "Physical unit": [[14, "physical-unit"]], "Default unit cell file name": [[14, "default-unit-cell-file-name"]], "Default displacement distance created": [[14, "default-displacement-distance-created"]], "Phono3py API": [[15, "phono3py-api"]], "Crystal structure": [[15, "crystal-structure"]], "Phono3py class": [[15, "phono3py-class"]], "Displacement dataset generation": [[15, "displacement-dataset-generation"]], "Supercell force calculation": [[15, "supercell-force-calculation"]], "Force constants calculation": [[15, "force-constants-calculation"]], "Non-analytical term correction parameters": [[15, "non-analytical-term-correction-parameters"]], "Regular grid for q-point sampling": [[15, "regular-grid-for-q-point-sampling"]], "Three integer values": [[15, "three-integer-values"]], "One value": [[15, "one-value"]], "3x3 integer matrix (experimental)": [[15, "x3-integer-matrix-experimental"]], "Phonon-phonon interaction calculation": [[15, "phonon-phonon-interaction-calculation"]], "Lattice thermal conductivity calculation": [[15, "lattice-thermal-conductivity-calculation"]], "Use of different supercell dimensions for 2nd and 3rd order FCs": [[15, "use-of-different-supercell-dimensions-for-2nd-and-3rd-order-fcs"]], "phono3py.load": [[15, "phono3py-load"]], "phono3py-load command": [[16, "phono3py-load-command"]], "Quantum ESPRESSO (pw) & phono3py calculation": [[17, "quantum-espresso-pw-phono3py-calculation"]], "References": [[18, "references"]], "Reviews": [[18, "reviews"]], "Averaged phonon-phonon interaction strength": [[18, "averaged-phonon-phonon-interaction-strength"]], "Cutoff-pair displacements": [[18, "cutoff-pair-displacements"]], "Self-energy, spectral function, joint-density of states": [[18, "self-energy-spectral-function-joint-density-of-states"]], "Tips": [[19, "tips"]], "Brillouin zone summation": [[19, "brillouin-zone-summation"]], "Importance of numerical quality of force constants": [[19, "importance-of-numerical-quality-of-force-constants"]], "A practical way to check lattice thermal conductivity result": [[19, "a-practical-way-to-check-lattice-thermal-conductivity-result"]], "Displacement distance of atoms": [[19, "displacement-distance-of-atoms"]], "File format compatibility with phonopy": [[19, "file-format-compatibility-with-phonopy"]], "TURBOMOLE & phono3py calculation": [[20, "turbomole-phono3py-calculation"]], "VASP & phono3py calculation": [[21, "vasp-phono3py-calculation"]], "Solution of the Wigner transport equation": [[22, "solution-of-the-wigner-transport-equation"]], "Solution of the WTE, scattering in the RTA approximation": [[22, "solution-of-the-wte-scattering-in-the-rta-approximation"]], "Solution of the WTE, exact treatment of scattering": [[22, "solution-of-the-wte-exact-treatment-of-scattering"]], "Computational cost": [[22, "computational-cost"]], "Workload distribution": [[24, "workload-distribution"]], "How to do it": [[24, "how-to-do-it"]], "A convenient script": [[24, "a-convenient-script"]]}, "indexentries": {}})
\ No newline at end of file
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"Sep-26-2015: version 0.9.13": [[2, "sep-26-2015-version-0-9-13"]], "Aug-12-2015: version 0.9.12": [[2, "aug-12-2015-version-0-9-12"]], "Jun-18-2015: version 0.9.10.1": [[2, "jun-18-2015-version-0-9-10-1"]], "Jun-17-2015: version 0.9.10": [[2, "jun-17-2015-version-0-9-10"]], "Changes in version 0.9.7": [[2, "changes-in-version-0-9-7"]], "Changes in version 0.9.6": [[2, "changes-in-version-0-9-6"]], "Changes in version 0.9.5": [[2, "changes-in-version-0-9-5"]], "Changes in version 0.9.4": [[2, "changes-in-version-0-9-4"]], "Changes in version 0.8.11": [[2, "changes-in-version-0-8-11"]], "Changes in version 0.8.10": [[2, "changes-in-version-0-8-10"]], "Changes in version 0.8.2": [[2, "changes-in-version-0-8-2"]], "Changes in version 0.8.0": [[2, "changes-in-version-0-8-0"]], "Changes in version 0.7.6": [[2, "changes-in-version-0-7-6"]], "Changes in version 0.7.2": [[2, "changes-in-version-0-7-2"]], "Changes in version 0.7.1": [[2, "changes-in-version-0-7-1"]], "Changes in version 0.6.0": [[2, "changes-in-version-0-6-0"]], "How to cite phono3py": [[3, "how-to-cite-phono3py"]], "Citation of phono3py": [[3, "citation-of-phono3py"]], "Citation of direct solution of LBTE (--lbte)": [[3, "citation-of-direct-solution-of-lbte-lbte"]], "Citation of solution of the Wigner transport equation (--wigner)": [[3, "citation-of-solution-of-the-wigner-transport-equation-wigner"]], "Command options / Setting tags": [[4, "command-options-setting-tags"]], "Input cell file name": [[4, "input-cell-file-name"]], "-c (CELL_FILENAME)": [[4, "c-cell-filename"]], "Calculator interface": [[4, "calculator-interface"]], "--qe (CALCULATOR = QE)": [[4, "qe-calculator-qe"]], "--crystal (CALCULATOR = CRYSTAL)": [[4, "crystal-calculator-crystal"]], "--turbomole (CALCULATOR = TURBOMOLE)": [[4, "turbomole-calculator-turbomole"]], "Utilities to create default input files": [[4, "utilities-to-create-default-input-files"]], "--cf3 (command option only)": [[4, "cf3-command-option-only"]], "--cf3-file (command option only)": [[4, "cf3-file-command-option-only"]], "--cf2 (command option only)": [[4, "cf2-command-option-only"]], "--cfz (command option only)": [[4, "cfz-command-option-only"]], "--fs2f2 or --force-sets-to-forces-fc2 (command option only)": [[4, "fs2f2-or-force-sets-to-forces-fc2-command-option-only"]], "--cfs or --create-force-sets (command option only)": [[4, "cfs-or-create-force-sets-command-option-only"]], "Supercell, primitive cell, masses, magnetic moments": [[4, "supercell-primitive-cell-masses-magnetic-moments"]], "--dim (DIM)": [[4, "dim-dim"]], "--dim-fc2 (DIM_FC2)": [[4, "dim-fc2-dim-fc2"]], "--pa, --primitive-axes (PRIMITIVE_AXES)": [[4, "pa-primitive-axes-primitive-axes"]], "--mass (MASS)": [[4, "mass-mass"]], "--magmom (MAGMOM)": [[4, "magmom-magmom"]], "Displacement creation": [[4, "displacement-creation"]], "-d (CREATE_DISPLACEMENTS = .TRUE.)": [[4, "d-create-displacements-true"]], "--amplitude (DISPLACEMENT_DISTANCE)": [[4, "amplitude-displacement-distance"]], "Force constants": [[4, "force-constants"]], "--cfc or --compact-fc (COMPACT_FC = .TRUE.)": [[4, "cfc-or-compact-fc-compact-fc-true"]], "--sym-fc (FC_SYMMETRY = .TRUE.)": [[4, "sym-fc-fc-symmetry-true"]], "--cutoff-fc3 or --cutoff-fc3-distance (CUTOFF_FC3_DISTANCE)": [[4, "cutoff-fc3-or-cutoff-fc3-distance-cutoff-fc3-distance"]], "--cutoff-pair or --cutoff-pair-distance (CUTOFF_PAIR_DISTANCE)": [[4, "cutoff-pair-or-cutoff-pair-distance-cutoff-pair-distance"]], "--alm": [[4, "alm"]], "Reciprocal space sampling mesh and grid points, and band indices": [[4, "reciprocal-space-sampling-mesh-and-grid-points-and-band-indices"]], "--mesh (MESH or MESH_NUMBERS)": [[4, "mesh-mesh-or-mesh-numbers"]], "--gp (GRID_POINTS)": [[4, "gp-grid-points"]], "--ga (GRID_ADDRESSES)": [[4, "ga-grid-addresses"]], "--bi (BAND_INDICES)": [[4, "bi-band-indices"]], "--wgp (command option only)": [[4, "wgp-command-option-only"]], "--stp (command option only)": [[4, "stp-command-option-only"]], "Brillouin zone integration": [[4, "brillouin-zone-integration"]], "--thm (TETRAHEDRON = .TRUE.)": [[4, "thm-tetrahedron-true"]], "--sigma (SIGMA)": [[4, "sigma-sigma"]], "--sigma-cutoff (SIGMA_CUTOFF_WIDTH)": [[4, "sigma-cutoff-sigma-cutoff-width"]], "--full-pp (FULL_PP = .TRUE.)": [[4, "full-pp-full-pp-true"]], "Methods to solve phonon Boltzmann equation and Wigner formulation": [[4, "methods-to-solve-phonon-boltzmann-equation-and-wigner-formulation"]], "--br (BTERTA = .TRUE.)": [[4, "br-bterta-true"]], "--lbte (LBTE = .TRUE.)": [[4, "lbte-lbte-true"]], "--wigner": [[4, "wigner"]], "Scattering": [[4, "scattering"]], "--isotope (ISOTOPE =.TRUE.)": [[4, "isotope-isotope-true"]], "--mass-variances or --mv (MASS_VARIANCES)": [[4, "mass-variances-or-mv-mass-variances"]], "--boundary-mfp, --bmfp (BOUNDARY_MFP)": [[4, "boundary-mfp-bmfp-boundary-mfp"]], "--ave-pp (USE_AVE_PP = .TRUE.)": [[4, "ave-pp-use-ave-pp-true"]], "--const-ave-pp (CONST_AVE_PP = .TRUE.)": [[4, "const-ave-pp-const-ave-pp-true"]], "--nu (N_U = .TRUE.)": [[4, "nu-n-u-true"]], "--scattering-event-class (SCATTERING_EVENT_CLASS)": [[4, "scattering-event-class-scattering-event-class"]], "Temperature": [[4, "temperature"]], "--ts (TEMPERATURES): Temperatures": [[4, "ts-temperatures-temperatures"]], "--tmax, --tmin, --tstep (TMAX, TMIN, TSTEP)": [[4, "tmax-tmin-tstep-tmax-tmin-tstep"]], "Non-analytical term correction": [[4, "non-analytical-term-correction"]], "--nac (NAC = .TRUE.)": [[4, "nac-nac-true"]], "--q-direction (Q_DIRECTION)": [[4, "q-direction-q-direction"]], "Imaginary and real parts of self energy": [[4, "imaginary-and-real-parts-of-self-energy"]], "--ise (IMAG_SELF_ENERGY = .TRUE.)": [[4, "ise-imag-self-energy-true"]], "--rse (REAL_SELF_ENERGY = .TRUE.)": [[4, "rse-real-self-energy-true"]], "Spectral function": [[4, "spectral-function"]], "--spf (SPECTRAL_FUNCTION = .TRUE.)": [[4, "spf-spectral-function-true"]], "Joint density of states (JDOS) and weighted-JDOS": [[4, "joint-density-of-states-jdos-and-weighted-jdos"]], "--jdos (JOINT_DOS = .TRUE.)": [[4, "jdos-joint-dos-true"]], "Sampling frequency for distribution functions": [[4, "sampling-frequency-for-distribution-functions"]], "--num-freq-points, --freq-pitch (NUM_FREQUENCY_POINTS)": [[4, "num-freq-points-freq-pitch-num-frequency-points"]], "Mode-Gruneisen parameter from 3rd order force constants": [[4, "mode-gruneisen-parameter-from-3rd-order-force-constants"]], "--gruneisen (GRUNEISEN = .TRUE.)": [[4, "gruneisen-gruneisen-true"]], "File I/O": [[4, "file-i-o"]], "--fc2 (READ_FC2 = .TRUE.)": [[4, "fc2-read-fc2-true"]], "--fc3 (READ_FC3 = .TRUE.)": [[4, "fc3-read-fc3-true"]], "--write-gamma (WRITE_GAMMA = .TRUE.)": [[4, "write-gamma-write-gamma-true"]], "--read-gamma (READ_GAMMA = .TRUE.)": [[4, "read-gamma-read-gamma-true"]], "--write-gamma-detail (WRITE_GAMMA_DETAIL = .TRUE.)": [[4, "write-gamma-detail-write-gamma-detail-true"]], "--write-phonon (WRITE_PHONON = .TRUE.)": [[4, "write-phonon-write-phonon-true"]], "--read-phonon (READ_PHONON = .TRUE.)": [[4, "read-phonon-read-phonon-true"]], "--write-pp (WRITE_PP = .TRUE.) and --read-pp (READ_PP = .TRUE.)": [[4, "write-pp-write-pp-true-and-read-pp-read-pp-true"]], "--hdf5-compression (command option only)": [[4, "hdf5-compression-command-option-only"]], "-o (command option only)": [[4, "o-command-option-only"]], "-i (command option only)": [[4, "i-command-option-only"]], "--io (command option only)": [[4, "io-command-option-only"]], "CRYSTAL & phono3py calculation": [[5, "crystal-phono3py-calculation"]], "Workflow": [[5, "workflow"], [17, "workflow"], [20, "workflow"], [21, "workflow"], [23, "workflow"]], "Force constants calculation with cutoff pair-distance": [[6, "force-constants-calculation-with-cutoff-pair-distance"]], "What is cutff pair-distance in phono3py?": [[6, "what-is-cutff-pair-distance-in-phono3py"]], "Usage": [[6, "usage"]], "Creating supercells with displacements": [[6, "creating-supercells-with-displacements"]], "Supercell files": [[6, "supercell-files"]], "Special phono3py_disp.yaml": [[6, "special-phono3py-disp-yaml"]], "Making FORCES_FC3": [[6, "making-forces-fc3"]], "Running phonon-phonon interaction calculation": [[6, "running-phonon-phonon-interaction-calculation"]], "A script extract supercell IDs from phono3py_disp.yaml": [[6, "a-script-extract-supercell-ids-from-phono3py-disp-yaml"]], "Tests": [[6, "tests"]], "Si-PBE": [[6, "si-pbe"]], "AlN-LDA": [[6, "aln-lda"]], "Direct solution of linearized phonon Boltzmann equation": [[7, "direct-solution-of-linearized-phonon-boltzmann-equation"]], "How to use": [[7, "how-to-use"], [22, "how-to-use"]], "Memory usage": [[7, "memory-usage"]], "Work load distribution": [[7, "work-load-distribution"]], "Distribution of collision matrix": [[7, "distribution-of-collision-matrix"]], "Distribution of phonon-phonon interaction strengths": [[7, "distribution-of-phonon-phonon-interaction-strengths"]], "Cutoff parameter of pseudo inversion": [[7, "cutoff-parameter-of-pseudo-inversion"]], "Diagonalization solver interfaces": [[7, "diagonalization-solver-interfaces"]], "OpenBLAS or MKL linked scipy and numpy": [[7, "openblas-or-mkl-linked-scipy-and-numpy"]], "OpenBLAS or MKL via LAPACKE": [[7, "openblas-or-mkl-via-lapacke"]], "Solver choice for diagonalization": [[7, "solver-choice-for-diagonalization"]], "Examples": [[8, "examples"]], "External tools": [[9, "external-tools"]], "Phono3py-Power-Tools": [[9, "phono3py-power-tools"]], "Kinetic Collective Model": [[9, "kinetic-collective-model"]], "How to read the results stored in hdf5 files": [[10, "how-to-read-the-results-stored-in-hdf5-files"]], "How to use HDF5 python library": [[10, "how-to-use-hdf5-python-library"]], "Details of kappa-*.hdf5 file": [[10, "details-of-kappa-hdf5-file"]], "mesh": [[10, "mesh"]], "frequency": [[10, "frequency"]], "gamma": [[10, "gamma"]], "gamma_isotope": [[10, "gamma-isotope"]], "group_velocity": [[10, "group-velocity"]], "heat_capacity": [[10, "heat-capacity"]], "kappa": [[10, "kappa"]], "mode-kappa": [[10, "mode-kappa"]], "gv_by_gv": [[10, "gv-by-gv"]], "q-point": [[10, "q-point"]], "temperature": [[10, "temperature"]], "weight": [[10, "weight"]], "ave_pp": [[10, "ave-pp"]], "kappa_unit_conversion": [[10, "kappa-unit-conversion"]], "How to know grid point index number corresponding to grid address": [[10, "how-to-know-grid-point-index-number-corresponding-to-grid-address"]], "Welcome to phono3py": [[11, "welcome-to-phono3py"]], "Documentation": [[11, "documentation"]], "Mailing list": [[11, "mailing-list"]], "License": [[11, "license"]], "Contact": [[11, "contact"]], "Input / Output files": [[12, "input-output-files"]], "Intermediate text files": [[12, "intermediate-text-files"]], "phono3py_disp.yaml": [[12, "phono3py-disp-yaml"]], "FORCES_FC3": [[12, "forces-fc3"]], "FORCES_FC2": [[12, "forces-fc2"]], "HDF5 files": [[12, "hdf5-files"]], "kappa-*.hdf5": [[12, "kappa-hdf5"]], "fc3.hdf5": [[12, "fc3-hdf5"]], "fc2.hdf5": [[12, "fc2-hdf5"]], "gamma-*.hdf5": [[12, "gamma-hdf5"]], "gamma_detail-*.hdf5": [[12, "gamma-detail-hdf5"]], "Simple text file": [[12, "simple-text-file"]], "gammas-*.dat": [[12, "gammas-dat"]], "jdos-*.dat": [[12, "jdos-dat"]], "linewidth-*.dat": [[12, "linewidth-dat"]], "Installation": [[13, "installation"]], "Installation using conda": [[13, "installation-using-conda"]], "Installation from source code": [[13, "installation-from-source-code"]], "Build with automatic search of library configurations by cmake": [[13, "build-with-automatic-search-of-library-configurations-by-cmake"]], "Build with custom library configurations by site.cfg file": [[13, "build-with-custom-library-configurations-by-site-cfg-file"]], "Installation instruction of latest development version of phono3py": [[13, "installation-instruction-of-latest-development-version-of-phono3py"]], "Installation of LAPACKE": [[13, "installation-of-lapacke"]], "OpenBLAS provided by conda": [[13, "openblas-provided-by-conda"]], "Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS)": [[13, "netlib-lapacke-provided-by-ubuntu-package-manager-with-single-thread-blas"]], "Compiling Netlib LAPACKE": [[13, "compiling-netlib-lapacke"]], "Multithreading and its controlling by C macro": [[13, "multithreading-and-its-controlling-by-c-macro"]], "OpenMP library of gcc": [[13, "openmp-library-of-gcc"]], "Trouble shooting": [[13, "trouble-shooting"]], "Interfaces to calculators": [[14, "interfaces-to-calculators"]], "Calculator specific behaviors": [[14, "calculator-specific-behaviors"]], "Physical unit": [[14, "physical-unit"]], "Default unit cell file name": [[14, "default-unit-cell-file-name"]], "Default displacement distance created": [[14, "default-displacement-distance-created"]], "Phono3py API": [[15, "phono3py-api"]], "Crystal structure": [[15, "crystal-structure"]], "Phono3py class": [[15, "phono3py-class"]], "Displacement dataset generation": [[15, "displacement-dataset-generation"]], "Supercell force calculation": [[15, "supercell-force-calculation"]], "Force constants calculation": [[15, "force-constants-calculation"]], "Non-analytical term correction parameters": [[15, "non-analytical-term-correction-parameters"]], "Regular grid for q-point sampling": [[15, "regular-grid-for-q-point-sampling"]], "Three integer values": [[15, "three-integer-values"]], "One value": [[15, "one-value"]], "3x3 integer matrix (experimental)": [[15, "x3-integer-matrix-experimental"]], "Phonon-phonon interaction calculation": [[15, "phonon-phonon-interaction-calculation"]], "Lattice thermal conductivity calculation": [[15, "lattice-thermal-conductivity-calculation"]], "Use of different supercell dimensions for 2nd and 3rd order FCs": [[15, "use-of-different-supercell-dimensions-for-2nd-and-3rd-order-fcs"]], "phono3py.load": [[15, "phono3py-load"]], "phono3py-load command": [[16, "phono3py-load-command"]], "Quantum ESPRESSO (pw) & phono3py calculation": [[17, "quantum-espresso-pw-phono3py-calculation"]], "References": [[18, "references"]], "Reviews": [[18, "reviews"]], "Averaged phonon-phonon interaction strength": [[18, "averaged-phonon-phonon-interaction-strength"]], "Cutoff-pair displacements": [[18, "cutoff-pair-displacements"]], "Self-energy, spectral function, joint-density of states": [[18, "self-energy-spectral-function-joint-density-of-states"]], "Tips": [[19, "tips"]], "Brillouin zone summation": [[19, "brillouin-zone-summation"]], "Importance of numerical quality of force constants": [[19, "importance-of-numerical-quality-of-force-constants"]], "A practical way to check lattice thermal conductivity result": [[19, "a-practical-way-to-check-lattice-thermal-conductivity-result"]], "Displacement distance of atoms": [[19, "displacement-distance-of-atoms"]], "File format compatibility with phonopy": [[19, "file-format-compatibility-with-phonopy"]], "TURBOMOLE & phono3py calculation": [[20, "turbomole-phono3py-calculation"]], "VASP & phono3py calculation": [[21, "vasp-phono3py-calculation"]], "Solution of the Wigner transport equation": [[22, "solution-of-the-wigner-transport-equation"]], "Solution of the WTE, scattering in the RTA approximation": [[22, "solution-of-the-wte-scattering-in-the-rta-approximation"]], "Solution of the WTE, exact treatment of scattering": [[22, "solution-of-the-wte-exact-treatment-of-scattering"]], "Computational cost": [[22, "computational-cost"]], "Workload distribution": [[24, "workload-distribution"]], "How to do it": [[24, "how-to-do-it"]], "A convenient script": [[24, "a-convenient-script"]]}, "indexentries": {}})
\ No newline at end of file