diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 0676c38..c8e80b5 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/velph-command.doctree b/.doctrees/velph-command.doctree index 65cea94..cfd66df 100644 Binary files a/.doctrees/velph-command.doctree and b/.doctrees/velph-command.doctree differ diff --git a/.doctrees/velph-subcommands.doctree b/.doctrees/velph-subcommands.doctree index 2ef48ef..692a429 100644 Binary files a/.doctrees/velph-subcommands.doctree and b/.doctrees/velph-subcommands.doctree differ diff --git a/_sources/velph-command.md b/_sources/velph-command.md index 09f4df7..b43e888 100644 --- a/_sources/velph-command.md +++ b/_sources/velph-command.md @@ -46,6 +46,7 @@ Commands: transport Choose transport options. ``` +(velph_hints)= ## `velph hints` This command provides a quick reference of calculation steps. diff --git a/_sources/velph-subcommands.md b/_sources/velph-subcommands.md index f32e917..4ee53b5 100644 --- a/_sources/velph-subcommands.md +++ b/_sources/velph-subcommands.md @@ -1,11 +1,68 @@ (velph_subcommands)= # `velph` subcommands -`velph init` is +The `velph` subcommands, except for {ref}`velph_init` and {ref}`velph_hints`, +are explained on this page. + +The following subcommands must be executed in the directory containing the +`velph.toml` file. This ensures that the directories and files generated are +properly organized relative to the current directory where `velph.toml` is +located. + +In the following example, two `velph init` command operations generate two +different directories. The first operation performs crystal structure relaxation +in the `relax` directory. The second operation, using the relaxed crystal +structure, carries out additional calculations required for electron-phonon +interactions in the `calc` directory. Details about `velph-tmpl.toml` are +described in {ref}`velph_init_template`. + +``` +% ls +POSCAR-unitcell POTCAR velph-tmpl.toml +% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax +... +% cd relax +% velph relax generate +... +# Run VASP relaxation calculation +... +% cd .. +% ls +POSCAR-unitcell POTCAR relax/ velph-tmpl.toml +% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc +... +% cd calc +% ls +POTCAR velph.toml +% velph nac generate +VASP input files were made in "nac". +% ls +POTCAR nac/ velph.toml +... +# Run NAC calculation +... +% velph phelel init +Found "nac" directory. Read NAC params. +"phelel/phelel_disp.yaml" was generated. +VASP input files will be generated by "velph phelel generate". +% velph phelel generate +VASP input files were generated in "phelel/disp-000". +VASP input files were generated in "phelel/disp-001". +VASP input files were generated in "phelel/disp-002". +VASP input files were generated in "phelel/disp-003". +VASP input files were generated in "phelel/disp-004". +% ls +POTCAR nac/ phelel/ velph.toml +% velph phelel init +Found "nac" directory. Read NAC params. +"phelel/phelel_disp.yaml" was generated. +VASP input files will be generated by "velph phelel generate". +... +``` ## `velph phelel` -This command calculates the derivatives of local potentials and PAW strengths +This subcommand calculates the derivatives of local potentials and PAW strengths with respect to displacement, performing similar operations as steps 1 and 3 carried out by the `phelel` command in the {ref}`workflow `. @@ -25,10 +82,51 @@ carried out by the `phelel` command in the {ref}`workflow `. ## `velph relax` +It is recommended to create a project directory secific for relaxation +calculation, e.g., by + +``` +% ls +POSCAR-unitcell POTCAR velph-tmpl.toml +% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax +... +% cd relax +% ls +POTCAR velph.toml +% velph relax generate +... +``` + ### `velph relax generate` +This subcommand prepares VASP input files and a job script for crystal structure +relaxation. Multiple relaxation calculations can be performed. In such cases, +the `CONTCAR` from the previous calculation is used as the `POSCAR` for the next +calculation to generate a new set of VASP input files. + +``` +% ls +POTCAR velph.toml +% velph relax generate +VASP input files were made in "relax/iter1". +... +# Run VASP calculation in relax/iter1 +... +% ls +POTCAR relax/ velph.toml +% velph relax generate +"relax/iter1" exists. +"relax/iter1/CONTCAR" will be as new "POSCAR". +VASP input files were made in "relax/iter2". +... +``` + ## `velph nac` +This subcommand is used to calculate dielectric constant and Born effective +charges that are used for non-analytical term correction of phonon calculation +and treatment of long range term of electron phonon interaction. + ### `velph nac generate` ## `velph el_bands` diff --git a/objects.inv b/objects.inv index 5d6c19e..faa0de5 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/searchindex.js b/searchindex.js index f5b21f4..33f2b5e 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"--amplitude": [[6, "amplitude"]], "--cd, --create-derivatives": [[3, "cd-create-derivatives"]], "--cell-for-nac": [[6, "cell-for-nac"]], "--cell-for-relax": [[6, "cell-for-relax"]], "--dim": [[3, "dim"]], "--kspacing and --kspacing-dense": [[6, "kspacing-and-kspacing-dense"]], "--magmom": [[6, "magmom"]], "--max-num-atoms": [[6, "max-num-atoms"]], "--no-find-primitive": [[6, "no-find-primitive"]], "--phonopy-max-num-atoms and --phono3py-max-num-atoms": [[6, "phonopy-max-num-atoms-and-phono3py-max-num-atoms"]], "--pm": [[3, "pm"]], "--primitive-cell-choice": [[6, "primitive-cell-choice"]], "--symmetrize": [[6, "symmetrize"]], "--template-toml": [[6, "template-toml"]], "--tolerance": [[6, "tolerance"]], "--use-grg": [[6, "use-grg"]], "-c, --cell": [[3, "c-cell"]], "-d": [[3, "d"]], "Additional steps (Optional)": [[9, "additional-steps-optional"]], "Calculation of derivatives of potentials": [[3, 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"phelel command", "velph command", "velph example", "velph init", "velph init template", "velph subcommands", "Workflow of el-ph calculation"], "titleterms": {"0": 0, "2024": 0, "2025": 0, "31": 0, "5": 0, "6": 0, "7": 0, "8": 0, "9": 0, "addit": 9, "amplitud": 6, "atom": 6, "c": 3, "calcul": [3, 9], "cd": 3, "cell": [3, 6], "chang": 0, "choic": 6, "code": 2, "command": [2, 3, 4], "complet": 2, "contributor": 1, "creat": 3, "d": 3, "dec": 0, "default": 7, "dens": 6, "deriv": 3, "differenti": 8, "dim": 3, "displac": 3, "el": 9, "el_band": 8, "exampl": 5, "find": 6, "from": 2, "gener": [3, 8], "grg": 6, "hint": 4, "incar": 7, "init": [6, 7, 8], "instal": 2, "jan": 0, "kspace": 6, "licens": 1, "log": 0, "magmom": 6, "max": 6, "minim": 9, "nac": [6, 8], "nitisn": 5, "num": 6, "option": [6, 9], "ph": 9, "ph_band": 8, "phelel": [1, 2, 3, 8], "phono3pi": [6, 8], "phonopi": [6, 8], "plot": 8, "pm": 3, "potenti": 3, "primit": 6, "relax": [6, 8], "requir": 2, "schedul": 7, "section": 7, "set": 7, "shell": 2, "sourc": 2, "step": 9, "subcommand": [4, 8], "supercel": 3, "symmetr": 6, "templat": [6, 7], "toler": 6, "toml": [6, 7], "transport": 8, "us": 6, "velph": [2, 4, 5, 6, 7, 8], "version": 0, "workflow": 9}}) \ No newline at end of file diff --git a/velph-command.html b/velph-command.html index 6902b81..470aaa8 100644 --- a/velph-command.html +++ b/velph-command.html @@ -349,7 +349,7 @@

velph
-

velph hints#

+

velph hints#

This command provides a quick reference of calculation steps.

% velph hints
diff --git a/velph-subcommands.html b/velph-subcommands.html index d7c9dd1..cbd67be 100644 --- a/velph-subcommands.html +++ b/velph-subcommands.html @@ -345,10 +345,64 @@

Contents

velph subcommands#

-

velph init is

+

The velph subcommands, except for velph init and velph hints, +are explained on this page.

+

The following subcommands must be executed in the directory containing the +velph.toml file. This ensures that the directories and files generated are +properly organized relative to the current directory where velph.toml is +located.

+

In the following example, two velph init command operations generate two +different directories. The first operation performs crystal structure relaxation +in the relax directory. The second operation, using the relaxed crystal +structure, carries out additional calculations required for electron-phonon +interactions in the calc directory. Details about velph-tmpl.toml are +described in velph init template.

+
% ls
+POSCAR-unitcell  POTCAR  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
+...
+% cd relax
+% velph relax generate
+...
+# Run VASP relaxation calculation
+...
+% cd ..
+% ls
+POSCAR-unitcell  POTCAR  relax/  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc
+...
+% cd calc
+% ls
+POTCAR  velph.toml
+% velph nac generate
+VASP input files were made in "nac".
+% ls
+POTCAR  nac/  velph.toml
+...
+# Run NAC calculation
+...
+% velph phelel init
+Found "nac" directory. Read NAC params.
+"phelel/phelel_disp.yaml" was generated.
+VASP input files will be generated by "velph phelel generate".
+% velph phelel generate
+VASP input files were generated in "phelel/disp-000".
+VASP input files were generated in "phelel/disp-001".
+VASP input files were generated in "phelel/disp-002".
+VASP input files were generated in "phelel/disp-003".
+VASP input files were generated in "phelel/disp-004".
+% ls
+POTCAR  nac/  phelel/  velph.toml
+% velph phelel init
+Found "nac" directory. Read NAC params.
+"phelel/phelel_disp.yaml" was generated.
+VASP input files will be generated by "velph phelel generate".
+...
+
+

velph phelel#

-

This command calculates the derivatives of local potentials and PAW strengths +

This subcommand calculates the derivatives of local potentials and PAW strengths with respect to displacement, performing similar operations as steps 1 and 3 carried out by the phelel command in the workflow.

@@ -375,12 +429,48 @@

velph

velph relax#

+

It is recommended to create a project directory secific for relaxation +calculation, e.g., by

+
% ls
+POSCAR-unitcell  POTCAR  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
+...
+% cd relax
+% ls
+POTCAR  velph.toml
+% velph relax generate
+...
+
+

velph relax generate#

+

This subcommand prepares VASP input files and a job script for crystal structure +relaxation. Multiple relaxation calculations can be performed. In such cases, +the CONTCAR from the previous calculation is used as the POSCAR for the next +calculation to generate a new set of VASP input files.

+
% ls
+POTCAR  velph.toml
+% velph relax generate
+VASP input files were made in "relax/iter1".
+...
+# Run VASP calculation in relax/iter1
+...
+% ls
+POTCAR  relax/  velph.toml
+% velph relax generate
+"relax/iter1" exists.
+"relax/iter1/CONTCAR" will be as new "POSCAR".
+VASP input files were made in "relax/iter2".
+...
+
+

velph nac#

+

This subcommand is used to calculate dielectric constant and Born effective +charges that are used for non-analytical term correction of phonon calculation +and treatment of long range term of electron phonon interaction.

velph nac generate#