diff --git a/doc/changelog.rst b/doc/changelog.rst index 9ca1032c..e4a782be 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -184,7 +184,7 @@ Jan-4-2015: Version 1.9.2 without a unit cell structure file. The unit cell structure file is specified using ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag. See :ref:`force_calculators`, :ref:`wien2k_interface`, - :ref:`abinit_interface`, and :ref:`pwscf_interface`. + :ref:`abinit_interface`, and :ref:`qe_interface`. * For the ``gruneisen`` command, ``--factor``, ``--nomeshsym``, ``--wien2k``, ``--abinit``, and ``--pwscf`` options are implemented. See :ref:`gruneisen_calculators` and @@ -197,8 +197,8 @@ Jan-4-2015: Version 1.9.2 Oct-30-2014: Version 1.9.1.3 ----------------------------- -* Experimental support for Abinit. See :ref:`pwscf_mode` and - :ref:`pwscf_force_sets_option`. +* Experimental support for Abinit. See :ref:`qe_mode` and + :ref:`qe_force_sets_option`. Oct-29-2014: Version 1.9.1.2 ----------------------------- diff --git a/doc/command-options.rst b/doc/command-options.rst index 07463c60..0b13f3d7 100644 --- a/doc/command-options.rst +++ b/doc/command-options.rst @@ -80,11 +80,11 @@ tags. Choice of force calculator --------------------------- -Currently interfaces for VASP, Wien2k, Pwscf, Abinit, and Elk are -prepared. Wien2k, Pwscf, Abinit, Elk and CRYSTAL interfaces are invoked with -``--wienk2``, ``--pwscf``, ``--abinit``, ``--elk`` and ``--crystal`` options, -respectively, and if none of these options or ``--vasp`` option is -specified, VASP mode is invoked. +Currently interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT, +Elk, SIESTA, and CRYSTAL are prepared. These interfaces are invoked +with ``--vasp``, ``--wienk2``, ``--qe``, ``--abinit``, ``--elk``, +``--siesta``, and ``--crystal`` options, respectively, and nothing is +specified, ``--vasp`` is selected as the default interface. The details about these interfaces are found at :ref:`calculator_interfaces`. @@ -127,18 +127,19 @@ e.g., % phonopy --abinit -c NaCl.in band.conf -.. _pwscf_mode: +.. _qe_mode: -``--pwscf`` +``--qe`` ~~~~~~~~~~~~ -Pwscf mode is invoked with this option. Usually this option is used -with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to read Pwscf -input file that contains the unit cell crystal structure, e.g., +Quantum ESPRESSO mode is invoked with this option. Usually this option +is used with ``--cell`` (``-c``) option or ``CELL_FILENAME`` tag to +read QE/PWscf input file that contains the unit cell crystal structure, +e.g., :: - % phonopy --pwscf -c NaCl.in band.conf + % phonopy --qe -c NaCl.in band.conf .. _siesta_mode: @@ -208,12 +209,12 @@ Unit cell crystal structure file is specified with this tag. Without specifying this tag, default file name is searched in current directory. The default file names for the calculators are as follows:: - VASP | POSCAR - Wien2k | case.struct - Abinit | unitcell.in - Pwscf | unitcell.in - Elk | elk.in - CRYSTAL| crystal.o + VASP | POSCAR + WIEN2k | case.struct + ABINIT | unitcell.in + PWscf | unitcell.in + Elk | elk.in + CRYSTAL | crystal.o Create ``FORCE_SETS`` ---------------------- @@ -252,11 +253,11 @@ Attention: .. _abinit_force_sets_option: -Abinit interface +ABINIT interface ^^^^^^^^^^^^^^^^ -``FORCE_SETS`` file is created from ``disp.yaml`` and Abinit output -files (``*.out``). In the reading of forces in Abinit output files, +``FORCE_SETS`` file is created from ``disp.yaml`` and ABINIT output +files (``*.out``). In the reading of forces in ABINIT output files, forces in eV/Angstrom are read. The unit conversion factor is determined with this unit. @@ -265,19 +266,20 @@ determined with this unit. % phonopy --abinit -f disp-001/supercell.out disp-002/supercell.out ... -.. _pwscf_force_sets_option: +.. _qe_force_sets_option: -Pwscf interface -^^^^^^^^^^^^^^^^ +Quantum ESPRESSO interface +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -``FORCE_SETS`` file is created from ``disp.yaml`` and Pwscf output +``FORCE_SETS`` file is created from ``disp.yaml`` and PWscf output files. :: - % phonopy --pwscf -f disp-001/supercell.out disp-002/supercell.out ... + % phonopy --qe -f disp-001/supercell.out disp-002/supercell.out ... -Here ``*.out`` files are the saved texts of standard outputs of Pwscf calculations. +Here ``*.out`` files are the saved texts of standard outputs of PWscf +calculations. .. _wien2k_force_sets_option: @@ -294,7 +296,7 @@ http://www.wien2k.at/reg_user/unsupported/. file when creating supercell with displacements, and ``case.scf``'s, which are the WIEN2k output files. The order of displacements in ``disp.yaml`` file and the order of ``case.scf``'s -have to be same. **For Wien2k struct file, only negative atom index +have to be same. **For WIEN2k struct file, only negative atom index with the P lattice format is supported.** :: @@ -446,5 +448,5 @@ printed out and phonopy stops without going to phonon analysis. % phonopy --symmetry This tag can be used together with the ``--cell`` (``-c``), -``--abinit``, ``--pwscf``, ``--elk``, ``--wien2k``, ``--crystal`` or -``--primitive_axis`` option. +``--abinit``, ``--qe``, ``--elk``, ``--wien2k``, ``--siesta``, +``--crystal`` or ``--primitive_axis`` option. diff --git a/doc/crystal.rst b/doc/crystal.rst index f5f08b1a..a40ef80f 100644 --- a/doc/crystal.rst +++ b/doc/crystal.rst @@ -3,7 +3,7 @@ CRYSTAL & phonopy calculation ========================================= -CRYSTAL program package has a robust built-in phonon calculation +CRYSTAL program package has a robust built-in phonon calculation workflow. However, the Phonopy interface enables convenient access to many phonon-related properties, such as subsequent Phono3py calculations of lattice thermal conductivity. @@ -17,7 +17,7 @@ For optimization outputs, the final geometry in the file is read. If dielectric tensor and effective Born charges are present, the interface creates a BORN file for Non-analytical correction (:ref:`nac_tag`). -The recommended strategy is to carry out a Gamma-point frequency calculation +The recommended strategy is to carry out a Gamma-point frequency calculation with INTENS and INTCPHF. This produces all required quantities and also confirms that the structure optimization has converged to a true local minimum. @@ -28,10 +28,10 @@ How to run ---------- The workflow for a CRYSTAL-Phonopy calculation is outlined here using the -Si example found in ``example/Si-CRYSTAL``. +Si example found in ``example/Si-CRYSTAL``. -In this example, the CRYSTAL output file is ``crystal.o``. -This is the default for the CRYSTAL interface, so, the ``-c crystal.o`` +In this example, the CRYSTAL output file is ``crystal.o``. +This is the default for the CRYSTAL interface, so, the ``-c crystal.o`` parameter is not needed 1) Create supercells with :ref:`crystal_mode` option:: @@ -39,19 +39,19 @@ parameter is not needed % phonopy --crystal -d --dim="4 4 4" In this example, 4x4x4 supercells are created. For every supercell file, the - interface creates a .d12 input file and an .ext structure file. The files + interface creates a .d12 input file and an .ext structure file. The files ``supercell.d12/.ext`` contain the perfect supercell. The files ``supercell-xxx.d12/.ext`` (``xxx`` are numbers) contain the supercells - with displacements. File ``disp.yaml`` is also generated, containing information + with displacements. File ``disp.yaml`` is also generated, containing information about the supercell and the displacements. - In the case of the Si example, files ``supercell-001.d12`` and + In the case of the Si example, files ``supercell-001.d12`` and ``supercell-001.ext`` will be created. 2) To make valid CRYSTAL input files, there are two possible options: - a) Manually: modify the generated supercell-xxx.d12 files by replacing - the line ``Insert basis sets and parameters here`` with the + a) Manually: modify the generated supercell-xxx.d12 files by replacing + the line ``Insert basis sets and parameters here`` with the basis set and computational parameters. b) Recommended option: before generating the supercells, include a file named @@ -60,8 +60,8 @@ parameter is not needed When phonopy finds this file, it automatically generates complete CRYSTAL input files in the step 1 - Note that supercells with displacements must not be relaxed in the - force calculations, because atomic forces induced by a small atomic + Note that supercells with displacements must not be relaxed in the + force calculations, because atomic forces induced by a small atomic displacement are what we need for phonon calculation. To get accurate forces, TOLDEE parameter should be 10 or higher. Phonopy includes this parameter and the necessary GRADCAL keyword automatically in the inputs. @@ -71,19 +71,18 @@ parameter is not needed % runcry14 supercell-001.d12 -3) To create ``FORCE_SETS``, that is used by phonopy, +3) To create ``FORCE_SETS``, that is used by phonopy, the following phonopy command is executed:: % phonopy --crystal -f supercell-001.o Here ``.o`` files are the CRYSTAL output files from the force - calculations. saved text files of standard outputs of the - Pwscf calculations. All ``.o`` files corresponding to the generated - ``supercell-xxx.d12`` files have to be given in the above command. - To run this command, ``disp.yaml`` has to be located in the current - directory because the information on atomic displacements stored in - ``disp.yaml`` are used to generate ``FORCE_SETS``. See some more detail at - :ref:`crystal_force_sets_option`. + calculations. All ``.o`` files corresponding to the generated + ``supercell-xxx.d12`` files have to be given in the above command. + To run this command, ``disp.yaml`` has to be located in the current + directory because the information on atomic displacements stored in + ``disp.yaml`` are used to generate ``FORCE_SETS``. See some more + detail at :ref:`crystal_force_sets_option`. 4) Now, Phonopy post-prcessing commands can be run. ``FORCE_SETS`` is automatically read in. Create phonon dispersion plot with: @@ -187,4 +186,3 @@ The workflow is very similar to the Si example below: .. |crystal-band-nac| image:: NaCl-crystal-band-NAC.png :width: 33% - diff --git a/doc/examples.rst b/doc/examples.rst index b8b99f18..f7a06999 100644 --- a/doc/examples.rst +++ b/doc/examples.rst @@ -17,29 +17,29 @@ Si ``FORCE_SETS`` file creation for VASP ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -For the other calculators such as pwscf, abinit, etc, the way to +For the other calculators such as PWscf, ABINIT, etc, the way to create ``FORCE_SETS`` is found following :ref:`calculator_interfaces`. :: - % phonopy -f vasprun.xml - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + % phonopy -f vasprun.xml + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 0.9.4 - counter (file index): 1 (1) - + counter (file index): 1 (1) + FORCE_SETS has been created. - _ + _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| - + where ``vasprun.xml`` is the VASP output. @@ -49,13 +49,13 @@ DOS :: % phonopy -p mesh.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 0.9.4 Mesh sampling mode Settings: @@ -70,7 +70,7 @@ DOS |Si-DOS| - + Thermal properties ~~~~~~~~~~~~~~~~~~ @@ -78,13 +78,13 @@ Thermal properties % phonopy -t -p mesh.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 0.9.4 Mesh sampling mode Settings: @@ -111,7 +111,7 @@ Thermal properties :width: 50% |Si-props| - + NaCl ---- @@ -121,13 +121,13 @@ Band structure :: % phonopy -p band.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 0.9.1.4 Band structure mode Settings: @@ -151,21 +151,21 @@ Band structure Band structure with non-analytical term correction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - + This requires to prepare BORN file. :: % phonopy -p --nac band.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 1.4 - + Band structure mode Settings: Non-analytical term correction: on @@ -198,15 +198,15 @@ PDOS :: % phonopy -p pdos.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 1.6.2 - + Mesh sampling mode Settings: Sampling mesh: [41 41 41] @@ -218,12 +218,12 @@ PDOS Spacegroup: Fm-3m (225) Calculating force constants... Number of irreducible q-points: 1771 - _ + _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| - + .. |NaCl-PDOS| image:: NaCl-PDOS.png :width: 50% @@ -233,19 +233,19 @@ PDOS With non-analytical term correction, the PDOS may not change very much because it mainly affects phonon modes in the reciprocal region close to :math:`\Gamma` point. - + :: % phonopy --nac -p pdos.conf - _ - _ __ | |__ ___ _ __ ___ _ __ _ _ + _ + _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 1.6.2 - + Mesh sampling mode Settings: Non-analytical term correction: on @@ -258,7 +258,7 @@ region close to :math:`\Gamma` point. Spacegroup: Fm-3m (225) Calculating force constants... Number of irreducible q-points: 1771 - _ + _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | @@ -283,9 +283,9 @@ profile than that given by the smearing method. | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 1.9.2.1 - + Mesh sampling mode Settings: Non-analytical term correction: on @@ -325,9 +325,9 @@ Band structure and DOS or PDOS can be plotted on one figure together by | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ - + 1.9.2 - + Band structure and mesh sampling mode Settings: Non-analytical term correction: on @@ -350,7 +350,7 @@ Band structure and DOS or PDOS can be plotted on one figure together by ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | - \___|_| |_|\__,_| + \___|_| |_|\__,_| .. |NaCl-band-PDOS-NAC| image:: NaCl-band-PDOS-NAC.png :width: 50% @@ -371,7 +371,7 @@ MgB2 characters of ireducible representations | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 1.11.10 - + Python version 3.6.0 Spglib version 1.9.9 Ir-representation mode @@ -379,115 +379,115 @@ MgB2 characters of ireducible representations Supercell: [3 3 2] Spacegroup: P6/mmm (191) Computing force constants... - + ------------------------------- Irreducible representations ------------------------------- q-point: [ 0. 0. 0.] Point group: 6/mmm - + Original rotation matrices: - + 1 2 3 4 5 6 -------- -------- -------- -------- -------- -------- 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0 0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 - + 7 8 9 10 11 12 -------- -------- -------- -------- -------- -------- -1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0 0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 - + 13 14 15 16 17 18 -------- -------- -------- -------- -------- -------- 0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 - + 19 20 21 22 23 24 -------- -------- -------- -------- -------- -------- 0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 - + Transformation matrix: - + 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 - + Rotation matrices by transformation matrix: - + E i C6 S3 C3 S6 -------- -------- -------- -------- -------- -------- 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0 0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 - + C2 sgh C3 S6 C6 S3 -------- -------- -------- -------- -------- -------- -1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0 0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 - + C2' sgd C2'' sgv C2' sgd -------- -------- -------- -------- -------- -------- 0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 - + C2'' sgv C2' sgd C2'' sgv -------- -------- -------- -------- -------- -------- 0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 - + Character table: - + 1 ( -0.019): A2u ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) - + 2 ( 0.004): E1u ( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) - + 4 ( 9.953): E1u ( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) - + 6 ( 11.982): A2u ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) - + 7 ( 17.269): E2g ( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) - + 9 ( 20.565): B2g ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) - + _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| - + Al-QHA ------- diff --git a/doc/gruneisen.rst b/doc/gruneisen.rst index 3ad6a3b5..e7d52749 100644 --- a/doc/gruneisen.rst +++ b/doc/gruneisen.rst @@ -13,7 +13,7 @@ How to run It is necessary to run three phonon calculations. One is calculated at the equilibrium volume and the remaining two are calculated at the slightly larger volume and smaller volume than the equilibrium -volume. The unitcells at these volumes have to be fully relaxed under +volume. The unitcells at these volumes have to be fully relaxed under the constraint of each volume. Let files named ``POSCAR-unitcell``, ``FORCE_SETS`` (or ``FORCE_CONSTANTS`` @@ -64,13 +64,13 @@ plot. .. _gruneisen_calculators: -Abinit, Pwscf, Wien2k, and CRYSTAL interfaces ---------------------------------------------- +Abinit, Quantum ESPRESSO, Wien2k, and CRYSTAL interfaces +---------------------------------------------------------- -``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options can be specified -for corresponding calculators and the crystal structure file format -should be different from that of the VASP format. An Abinit example is -as follows:: +``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal`` options can be +specified for corresponding calculators and the crystal structure file +format should be different from that of the VASP format. An Abinit +example is as follows:: % phonopy-gruneisen orig plus minus --abinit --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/4 3/4 0 0 0 1/2 1/2 1/2 1/2 0.0 1/2" -p -c Si.in @@ -80,11 +80,11 @@ as follows:: Command options ---------------- -If one of ``--abinit``, ``--pwscf``, ``--wien2k``, or ``--crystal`` options is -specified, the interface mode is changed to it. The unit conversion -factor to THz is appropriately selected and its crystal structure file -format is accepted. If none of them is specified, as the VASP -interface mode is invoked as the default interface. +If one of ``--abinit``, ``--qe``, ``--wien2k``, or ``--crystal`` +options is specified, the interface mode is changed to it. The unit +conversion factor to THz is appropriately selected and its crystal +structure file format is accepted. If none of them is specified, as +the VASP interface mode is invoked as the default interface. The following command options can be used for all interface modes. They work similarly to those for ``phonopy`` script. diff --git a/doc/index.rst b/doc/index.rst index a0499401..d17513b1 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -46,12 +46,12 @@ The following features of phonopy are highlighted: - :ref:`Interfaces to calculators `: :ref:`VASP `, :ref:`VASP DFPT `, - :ref:`Abinit `, - :ref:`Pwscf `, - :ref:`Siesta `, + :ref:`ABINIT `, + :ref:`Quantu ESPRESSO `, + :ref:`SIESTA `, :ref:`Elk `, :ref:`FHI-aims `, - :ref:`Wien2k `, + :ref:`WIEN2k `, :ref:`CRYSTAL ` - :ref:`Python APIs ` @@ -104,7 +104,7 @@ Mailing list For questions, bug reports, and comments, please visit https://lists.sourceforge.net/lists/listinfo/phonopy-users to -subscribe the phonopy mailing list +subscribe the phonopy mailing list and send them to phonopy-users@lists.sourceforge.net. Message body including attached files has to be smaller than 300 KB. diff --git a/doc/interfaces.rst b/doc/interfaces.rst index 4726b2fc..893f6617 100644 --- a/doc/interfaces.rst +++ b/doc/interfaces.rst @@ -3,9 +3,10 @@ Interfaces to calculators ========================== -The interfaces for VASP, Wien2k, Pwscf, Abinit, Elk and CRYSTAL are built in -to the usual phonopy command. See the command options and how to -invoke each of them at :ref:`force_calculators`. +The interfaces for VASP, WIEN2k, Quantum ESPRESSO (QE), ABINIT, Elk, +SIESTA, and CRYSTAL are built in to the usual phonopy command. See the +command options and how to invoke each of them at +:ref:`force_calculators`. Physical unit system for calculator ------------------------------------ @@ -15,11 +16,11 @@ Physical unit systems used for the calculators are as follows:: | Distance Atomic mass Force Force constants ----------------------------------------------------------------- VASP | Angstrom AMU eV/Angstrom eV/Angstrom^2 - Wien2k | au (bohr) AMU mRy/au mRy/au^2 - Pwscf | au (bohr) AMU Ry/au Ry/au^2 - Abinit | au (bohr) AMU eV/Angstrom eV/Angstrom.au - Siesta | au (bohr) AMU eV/Angstrom eV/Angstrom.au - elk | au (bohr) AMU hartree/au hartree/au^2 + WIEN2k | au (bohr) AMU mRy/au mRy/au^2 + QE | au (bohr) AMU Ry/au Ry/au^2 + ABINIT | au (bohr) AMU eV/Angstrom eV/Angstrom.au + SIESTA | au (bohr) AMU eV/Angstrom eV/Angstrom.au + Elk | au (bohr) AMU hartree/au hartree/au^2 CRYSTAL | Angstrom AMU eV/Angstrom eV/Angstrom^2 For these sets of physical properties, phonon frequency is calculated @@ -35,10 +36,10 @@ Without specifying ``-c`` option, default file name for unit cell is used as shown below:: VASP | POSCAR - Wien2k | case.struct - Pwscf | unitcell.in - Abinit | unitcell.in - Siesta | input.fdf + WIEN2k | case.struct + QE | unitcell.in + ABINIT | unitcell.in + SIESTA | input.fdf Elk | elk.in CRYSTAL | crystal.o @@ -52,13 +53,28 @@ option. The default value is dependent on calculator, and the list is shown below:: VASP | 0.01 Angstrom - Wien2k | 0.02 au (bohr) - Pwscf | 0.02 au (bohr) - Abinit | 0.02 au (bohr) - Siesta | 0.02 au (bohr) + WIEN2k | 0.02 au (bohr) + QE | 0.02 au (bohr) + ABINIT | 0.02 au (bohr) + SIESTA | 0.02 au (bohr) Elk | 0.02 au (bohr) CRYSTAL | 0.01 Angstrom +.. _frequency_default_value_interfaces: + +Default unit conversion factor of phonon frequency to THz +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +:: + + VASP | 15.633302 + WIEN2k | 3.44595837 + QE | 108.97077 + ABINIT | 21.49068 + SIESTA | 21.49068 + Elk | 154.10794 + CRYSTAL | 15.633302 + .. _nac_default_value_interfaces: Default unit conversion factor for non-analytical term correction @@ -67,10 +83,10 @@ Default unit conversion factor for non-analytical term correction :: VASP | 14.399652 - Wien2k | 2000 - Pwscf | 2 - Abinit | 51.422090 - Siesta | 51.422090 + WIEN2k | 2000 + QE | 2 + ABINIT | 51.422090 + SIESTA | 51.422090 Elk | 1 CRYSTAL | 14.399652 diff --git a/doc/procedure.rst b/doc/procedure.rst index 2a533cb6..d9bbea96 100644 --- a/doc/procedure.rst +++ b/doc/procedure.rst @@ -3,6 +3,6 @@ Short tutorials ================ -Tutorials for different force calculators, VASP, WIEN2k, PWscf (QE), -ABINIT, SIESTA, Elk, and, CRYSTAL, are found at +Tutorials for different force calculators, VASP, WIEN2k, Quantum +ESPRESSO, ABINIT, SIESTA, Elk, and, CRYSTAL, are found at :ref:`tutorials_for_calculators`. diff --git a/doc/pwscf.rst b/doc/pwscf.rst index 9d334b70..2e0ab7b2 100644 --- a/doc/pwscf.rst +++ b/doc/pwscf.rst @@ -1,9 +1,9 @@ -.. _pwscf_interface: +.. _qe_interface: -Pwscf & phonopy calculation -========================================= +Quantum ESPRESSO (QE) & phonopy calculation +============================================ -Quantum espresso package itself has a set of the phonon calculation +Quantum ESPRESSO package itself has a set of the phonon calculation system. But the document here explains how to calculate phonons using phonopy, i.e., using the finite displacement and supercell approach. @@ -16,7 +16,7 @@ More tags may be supported on request. :: - nat, ntyp, ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS + nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS How to run ---------- @@ -25,9 +25,9 @@ The procedure of Pwscf-phonopy calculation is shown below using the NaCl example found in ``example/NaCl-pwscf`` directory. 1) Read a Pwscf input file and create supercells with - :ref:`pwscf_mode` option:: + :ref:`qe_mode` option:: - % phonopy --pwscf -d --dim="2 2 2" -c NaCl.in + % phonopy --qe -d --dim="2 2 2" -c NaCl.in In this example, 2x2x2 supercells are created. ``supercell.in`` and ``supercell-xxx.in`` (``xxx`` are numbers) give the perfect @@ -57,10 +57,10 @@ NaCl example found in ``example/NaCl-pwscf`` directory. % mpirun pw.x -i NaCl-001.in |& tee NaCl-001.out % mpirun pw.x -i NaCl-002.in |& tee NaCl-002.out -3) To create ``FORCE_SETS``, that is used by phonopy, +3) To create ``FORCE_SETS``, that is used by phonopy, the following phonopy command is executed:: - % phonopy --pwscf -f NaCl-001.out NaCl-002.out + % phonopy --qe -f NaCl-001.out NaCl-002.out Here ``.out`` files are the saved text files of standard outputs of the Pwscf calculations. If more supercells with displacements were @@ -69,7 +69,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory. the current directory because the information on atomic displacements stored in ``disp.yaml`` are used to generate ``FORCE_SETS``. See some more detail at - :ref:`pwscf_force_sets_option`. + :ref:`qe_force_sets_option`. 4) Now post-process of phonopy is ready to run. The unit cell file used in the step 1 has to be specified but ``FORCE_SETS`` is @@ -77,7 +77,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory. :: - % phonopy --pwscf -c NaCl.in -p band.conf + % phonopy --qe -c NaCl.in -p band.conf _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | @@ -85,7 +85,7 @@ NaCl example found in ``example/NaCl-pwscf`` directory. | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 1.11.0 - + Python version 2.7.12 Spglib version 1.9.2 Calculator interface: pwscf @@ -113,15 +113,15 @@ NaCl example found in ``example/NaCl-pwscf`` directory. |pwscf-band| .. |pwscf-band| image:: NaCl-pwscf-band.png - :width: 50% + :width: 50% - ``--pwscf -c NaCl.in`` is specific for the Pwscf-phonopy + ``--qe -c NaCl.in`` is specific for the Pwscf-phonopy calculation but the other settings are totally common among calculator interfaces such as :: - % phonopy --pwscf -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file] + % phonopy --qe -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file] For settings and command options, see :ref:`setting_tags` and :ref:`command_options`, respectively, and @@ -133,7 +133,7 @@ Non-analytical term correction (Optional) To activate non-analytical term correction, :ref:`born_file` is required. This file contains the information of Born effective charge and dielectric constant. These physical values are also obtained from -the pwscf (``pw.x``) & phonon (``ph.x``) codes in quantum-espresso +the pwscf (``pw.x``) & phonon (``ph.x``) codes in Quantum ESPRESSO package. There are two steps. The first step is usual self-consistent field (SCF) calculation by and the second step is running its response function calculations @@ -206,13 +206,13 @@ be something like below:: 1.105385 0 0 0 1.105385 0 0 0 1.105385 -1.105385 0 0 0 -1.105385 0 0 0 -1.105385 -Once this is made, the non-analytical term correction is included +Once this is made, the non-analytical term correction is included just adding the ``--nac`` option as follows:: - % phonopy --pwscf --nac -c NaCl.in -p band.conf + % phonopy --qe --nac -c NaCl.in -p band.conf |pwscf-band-nac| .. |pwscf-band-nac| image:: NaCl-pwscf-band-NAC.png - :width: 50% + :width: 50% diff --git a/doc/setting-tags.rst b/doc/setting-tags.rst index fd6b7827..df7b6ef3 100644 --- a/doc/setting-tags.rst +++ b/doc/setting-tags.rst @@ -198,11 +198,11 @@ it doesn't work for derived values like thermal properties and mean square displacements. The default values for calculators are those to convert frequency -units to THz. The default conversion factors for ``wien2k``, -``abinit``, ``pwscf``, ``elk``, and CRYSTAL are 3.44595, 21.49068, 108.9708, -154.1079, and 15.633302 respectively. These are determined following the physical -unit systems of the calculators. How to calcualte these conversion -factors is explained at :ref:`physical_unit_conversion`. +units to THz. The default conversion factors are shown at +:ref:`frequency_default_value_interfaces`. These are determined +following the physical unit systems of the calculators. How to +calcualte these conversion factors is explained at +:ref:`physical_unit_conversion`. Displacement creation tags --------------------------