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Merge pull request #263 from Exabyte-io/update/SOF-6827
SOF-6827: 3pse schemas
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| { | ||
| "&CONTROL": { | ||
| "calculation": "scf", | ||
| "title": "", | ||
| "verbosity": "low", | ||
| "restart_mode": "from_scratch", | ||
| "wf_collect": true, | ||
| "tstress": true, | ||
| "tprnfor": true, | ||
| "outdir": "{{ JOB_WORK_DIR }}/outdir", | ||
| "wfcdir": "{{ JOB_WORK_DIR }}/outdir", | ||
| "prefix": "__prefix__", | ||
| "pseudo_dir": "{{ JOB_WORK_DIR }}/pseudo" | ||
| }, | ||
| "&SYSTEM": { | ||
| "ibrav": 0, | ||
| "nat": 2, | ||
| "ntyp": 2, | ||
| "ecutwfc": 40, | ||
| "ecutrho": 200, | ||
| "occupations": "smearing", | ||
| "degauss": 0.005, | ||
| "starting_magnetization": [ | ||
| 0.01, | ||
| 0.02 | ||
| ], | ||
| "Hubbard_occ": [ | ||
| [ | ||
| 1, | ||
| 1, | ||
| 0.00 | ||
| ], | ||
| [ | ||
| 1, | ||
| 2, | ||
| 0.02 | ||
| ] | ||
| ] | ||
| }, | ||
| "&ELECTRONS": { | ||
| "diagonalization": "david", | ||
| "diago_david_ndim": 4, | ||
| "diago_full_acc": true, | ||
| "mixing_beta": 0.3, | ||
| "startingwfc": "atomic+random" | ||
| }, | ||
| "&IONS": null, | ||
| "&CELL": null, | ||
| "ATOMIC_SPECIES": { | ||
| "values": [ | ||
| { | ||
| "X": "Cs", | ||
| "Mass_X": 132.90543, | ||
| "PseudoPot_X": "Cs.upf" | ||
| }, | ||
| { | ||
| "X": "Cl", | ||
| "Mass_X": 35.4527, | ||
| "PseudoPot_X": "Cl.upf" | ||
| } | ||
| ] | ||
| }, | ||
| "CELL_PARAMETERS": { | ||
| "card_option": "angstrom", | ||
| "values": { | ||
| "v1": [ | ||
| 4.324582724, | ||
| 0.000000000, | ||
| 2.496799000 | ||
| ], | ||
| "v2": [ | ||
| 1.441527575, | ||
| 4.077255694, | ||
| 2.496799000 | ||
| ], | ||
| "v3": [ | ||
| 0.000000000, | ||
| 0.000000000, | ||
| 4.993598000 | ||
| ] | ||
| } | ||
| }, | ||
| "K_POINTS": { | ||
| "card_option": "automatic", | ||
| "values": { | ||
| "nk1": 2, | ||
| "nk2": 2, | ||
| "nk3": 2, | ||
| "sk1": 0, | ||
| "sk2": 0, | ||
| "sk3": 0 | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| { | ||
| "$id": "3pse/file/applications/espresso/7.2/pw.x", | ||
| "$schema": "http://json-schema.org/draft-04/schema#", | ||
| "title": "pwx main schema", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "&CONTROL": { | ||
| "$ref": "./pw.x/control.json" | ||
| }, | ||
| "&SYSTEM": { | ||
| "$ref": "./pw.x/system.json" | ||
| }, | ||
| "&ELECTRONS": { | ||
| "$ref": "./pw.x/electrons.json" | ||
| }, | ||
| "&IONS": { | ||
| "oneOf": [ | ||
| { | ||
| "$ref": "./pw.x/ions.json" | ||
| }, | ||
| { | ||
| "type": "null" | ||
| } | ||
| ] | ||
| }, | ||
| "&CELL": { | ||
| "oneOf": [ | ||
| { | ||
| "$ref": "./pw.x/cell.json" | ||
| }, | ||
| { | ||
| "type": "null" | ||
| } | ||
| ] | ||
| }, | ||
| "ATOMIC_SPECIES": { | ||
| "$ref": "./pw.x/atomic_species.json" | ||
| }, | ||
| "ATOMIC_POSITIONS": { | ||
| "$ref": "./pw.x/atomic_positions.json" | ||
| }, | ||
| "K_POINTS": { | ||
| "$ref": "./pw.x/k_points.json" | ||
| }, | ||
| "CELL_PARAMETERS": { | ||
| "$ref": "./pw.x/cell_parameters.json" | ||
| }, | ||
| "HUBBARD": { | ||
| "$ref": "./pw.x/hubbard.json" | ||
| } | ||
| } | ||
| } |
66 changes: 66 additions & 0 deletions
66
schema/3pse/file/applications/espresso/7.2/pw.x/atomic_positions.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| { | ||
| "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-positions", | ||
| "$schema": "http://json-schema.org/draft-04/schema#", | ||
| "title": "atomic positions schema", | ||
| "description": "https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm1493", | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "card_option": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "alat", | ||
| "bohr", | ||
| "angstrom", | ||
| "crystal", | ||
| "crystal_sg" | ||
| ], | ||
| "default": "alat" | ||
| }, | ||
| "values": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "X": { | ||
| "type": "string", | ||
| "description": "label of the atom as specified in ATOMIC_SPECIES" | ||
| }, | ||
| "x": { | ||
| "type": "number", | ||
| "description": "atomic positions" | ||
| }, | ||
| "y": { | ||
| "type": "number", | ||
| "description": "atomic positions" | ||
| }, | ||
| "z": { | ||
| "type": "number", | ||
| "description": "atomic positions" | ||
| }, | ||
| "if_pos(1)": { | ||
| "$ref": "../../../../../../core/primitive/integer_one_or_zero.json", | ||
| "default": 1, | ||
| "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run." | ||
| }, | ||
| "if_pos(2)": { | ||
| "$ref": "../../../../../../core/primitive/integer_one_or_zero.json", | ||
| "default": 1, | ||
| "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run." | ||
| }, | ||
| "if_pos(3)": { | ||
| "$ref": "../../../../../../core/primitive/integer_one_or_zero.json", | ||
| "default": 1, | ||
| "description": "component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in MD dynamics or structural optimization run." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "x", | ||
| "y", | ||
| "z" | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } |
30 changes: 30 additions & 0 deletions
30
schema/3pse/file/applications/espresso/7.2/pw.x/atomic_species.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| { | ||
| "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-species", | ||
| "$schema": "http://json-schema.org/draft-04/schema#", | ||
| "title": "atomic species schema", | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "values": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "X": { | ||
| "type": "string", | ||
| "description": "label of the atom. Acceptable syntax: chemical symbol X (1 or 2 characters, case-insensitive) or chemical symbol plus a number or a letter, as in \"Xn\" (e.g. Fe1) or \"X_*\" or \"X-*\" (e.g. C1, C_h; max total length cannot exceed 3 characters)" | ||
| }, | ||
| "Mass_X": { | ||
| "type": "number", | ||
| "description": "mass of the atomic species [amu: mass of C = 12]. Used only when performing Molecular Dynamics run or structural optimization runs using Damped MD. Not actually used in all other cases (but stored in data files, so phonon calculations will use these values unless other values are provided)" | ||
| }, | ||
| "PseudoPot_X": { | ||
| "type": "string", | ||
| "description": "PseudoPot_X" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| { | ||
| "$id": "3pse/file/applications/espresso/7.2/pw.x/cell", | ||
| "$schema": "http://json-schema.org/draft-04/schema#", | ||
| "title": "cell schema", | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "oneOf": [ | ||
| { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "cell_dynamics": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "none", | ||
| "sd", | ||
| "damp-pr", | ||
| "damp-w", | ||
| "bfgs" | ||
| ], | ||
| "default": "bfgs", | ||
| "description": "CASE ( calculation == 'vc-relax' )" | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "cell_dynamics": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "none", | ||
| "pr", | ||
| "w" | ||
| ], | ||
| "description": "CASE ( calculation == 'vc-md' )" | ||
| } | ||
| } | ||
| } | ||
| ], | ||
| "properties": { | ||
| "press": { | ||
| "type": "number", | ||
| "description": "Target pressure [KBar] in a variable-cell md or relaxation run.", | ||
| "default": 0 | ||
| }, | ||
| "wmass": { | ||
| "type": "number", | ||
| "description": "Fictitious cell mass [amu] for variable-cell simulations (both 'vc-md' and 'vc-relax'). Default: 0.75*Tot_Mass/pi**2 for Parrinello-Rahman MD; 0.75*Tot_Mass/pi**2/Omega**(2/3) for Wentzcovitch MD" | ||
| }, | ||
| "cell_factor": { | ||
| "type": "number", | ||
| "description": "Used in the construction of the pseudopotential tables. It should exceed the maximum linear contraction of the cell during a simulation. Default: 2.0 for variable-cell calculations, 1.0 otherwise" | ||
| }, | ||
| "press_conv_thr": { | ||
| "type": "number", | ||
| "default": 0.5, | ||
| "description": "Convergence threshold on the pressure for variable cell relaxation ('vc-relax' : note that the other convergence thresholds for ionic relaxation apply as well)." | ||
| }, | ||
| "cell_dofree": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "all", | ||
| "ibrav", | ||
| "a", | ||
| "b", | ||
| "c", | ||
| "fixa", | ||
| "fixb", | ||
| "fixc", | ||
| "x", | ||
| "y", | ||
| "xy", | ||
| "xz", | ||
| "xyz", | ||
| "shape", | ||
| "volume", | ||
| "2Dxy", | ||
| "2Dshape", | ||
| "epitaxial_ab", | ||
| "epitaxial_ac", | ||
| "epitaxial_bc" | ||
| ], | ||
| "default": "all", | ||
| "description": "Select which of the cell parameters should be moved" | ||
| } | ||
| } | ||
| } |
36 changes: 36 additions & 0 deletions
36
schema/3pse/file/applications/espresso/7.2/pw.x/cell_parameters.json
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|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| { | ||
| "$id": "3pse/file/applications/espresso/7.2/pw.x/cell-parameters", | ||
| "$schema": "http://json-schema.org/draft-04/schema#", | ||
| "title": "cell parameters schema", | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "card_option": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "alat", | ||
| "bohr", | ||
| "angstrom" | ||
| ], | ||
| "description": "label of the atom. Acceptable syntax: chemical symbol X (1 or 2 characters, case-insensitive) or chemical symbol plus a number or a letter, as in \"Xn\" (e.g. Fe1) or \"X_*\" or \"X-*\" (e.g. C1, C_h; max total length cannot exceed 3 characters)" | ||
| }, | ||
| "values": { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "v1": { | ||
| "$ref": "../../../../../../core/primitive/array_of_3_numbers.json", | ||
| "description": "1st lattice vector" | ||
| }, | ||
| "v2": { | ||
| "$ref": "../../../../../../core/primitive/array_of_3_numbers.json", | ||
| "description": "2nd lattice vector" | ||
| }, | ||
| "v3": { | ||
| "$ref": "../../../../../../core/primitive/array_of_3_numbers.json", | ||
| "description": "3rd lattice vector" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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