Feature: Add readin-json support

[grysgreat]

Added the readin part of the information output in the abacus-json tree

Linked Issue

Fix #3646

Any changes of core modules? (ignore if not applicable)

• codes in module_io/json_output.

[pxlxingliang]

Hi, @grysgreat Could you please run an example using your codes and paste the new contents of abacus.json?

[grysgreat]

Hi, @grysgreat Could you please run an example using your codes and paste the new contents of abacus.json?

Sure! Here is the json file.

{
    "readin": {
        "stru": {
            "mag": [
                [
                    0.0,
                    0.0
                ]
            ],
            "pp": [
                "Si.pz-vbc.UPF"
            ],
            "orb": [
                "null"
            ],
            "label": [
                "Si"
            ],
            "element": [
                "Si"
            ],
            "coordinate": [
                [
                    0.0,
                    0.0,
                    0.0
                ],
                [
                    2.55,
                    2.55,
                    2.55
                ]
            ],
            "cell": [
                [
                    0.5,
                    0.5,
                    0.0
                ],
                [
                    0.5,
                    0.0,
                    0.5
                ],
                [
                    0.0,
                    0.5,
                    0.5
                ]
            ]
        }
    },
    "init": {
        "nkstot": 8,
        "nkstot_ibz": 8,
        "point_group": "T_d",
        "point_group_in_space": "O_h",
        "natom": 2,
        "nband": 14,
        "nelectron": 1,
        "nelectron_each_type": {
            "Si": 4
        }
    },
    "general_info": {
        "version": "v3.5.3",
        "commit": "c1fb6948b (Mon Feb 26 13:26:46 2024 +0800)",
        "device": "cpu",
        "mpi_num": 1,
        "omp_num": 2,
        "pseudo_dir": "../../../tests/PP_ORB",
        "orbital_dir": "",
        "stru_file": "STRU",
        "kpt_file": "",
        "start_time": "2024-02-28 20:37:08",
        "end_time": "2024-02-28 20:37:13"
    }
}

[pxlxingliang]

Hi, @grysgreat Could you please run an example using your codes and paste the new contents of abacus.json?

Sure! Here is the json file.

The mag should be a list of double, and each element is the value of each atom.
When the STRU do not define orbital, the value of orb should be null, but not a list of string "null"

[grysgreat]

Here is the new abacus.json:

{
    "init": {
        "element": {
            "Si1": "Si"
        },
        "orb": {
            "Si1": null
        },
        "pp": {
            "Si1": "Si.pz-vbc.UPF"
        },
        "coordinate": [
            [
                0.0,
                0.0,
                0.0
            ],
            [
                2.55,
                2.55,
                2.55
            ]
        ],
        "mag": [
            0.0,
            0.0
        ],
        "label": [
            "Si1"
        ],
        "cell": [
            [
                0.5,
                0.5,
                0.0
            ],
            [
                0.5,
                0.0,
                0.5
            ],
            [
                0.0,
                0.5,
                0.5
            ]
        ],
        "nkstot": 8,
        "nkstot_ibz": 8,
        "point_group": "T_d",
        "point_group_in_space": "O_h",
        "natom": 2,
        "nband": 14,
        "nelectron": 8,
        "nelectron_each_type": {
            "Si1": 4
        }
    },
    "general_info": {
        "version": "v3.5.3",
        "commit": "c1fb6948b (Mon Feb 26 13:26:46 2024 +0800)",
        "device": "cpu",
        "mpi_num": 1,
        "omp_num": 2,
        "pseudo_dir": "../../../tests/PP_ORB",
        "orbital_dir": "",
        "stru_file": "STRU",
        "kpt_file": "",
        "start_time": "2024-03-01 18:08:50",
        "end_time": "2024-03-01 18:08:55"
    }
}

[pxlxingliang]

Hi @grysgreat init/label should be a list of labels of each atom, and the order of label is same as that of coordinate.

[grysgreat]

Fix that , here is the new abacus.json:

{
    "init": {
        "element": {
            "Si1": "Si"
        },
        "orb": {
            "Si1": null
        },
        "pp": {
            "Si1": "Si.pz-vbc.UPF"
        },
        "coordinate": [
            [
                0.0,
                0.0,
                0.0
            ],
            [
                2.55,
                2.55,
                2.55
            ]
        ],
        "mag": [
            0.0,
            0.0
        ],
        "label": [
            "Si1",
            "Si1"
        ],
        "cell": [
            [
                0.5,
                0.5,
                0.0
            ],
            [
                0.5,
                0.0,
                0.5
            ],
            [
                0.0,
                0.5,
                0.5
            ]
        ],
        "nkstot": 8,
        "nkstot_ibz": 8,
        "point_group": "T_d",
        "point_group_in_space": "O_h",
        "natom": 2,
        "nband": 14,
        "nelectron": 8,
        "nelectron_each_type": {
            "Si1": 4
        }
    },
    "general_info": {
        "version": "v3.5.3",
        "commit": "ac2c41740 (Sun Mar 3 23:10:01 2024 +0800)",
        "device": "cpu",
        "mpi_num": 1,
        "omp_num": 2,
        "pseudo_dir": "../../../tests/PP_ORB",
        "orbital_dir": "",
        "stru_file": "STRU",
        "kpt_file": "",
        "start_time": "2024-03-05 16:42:08",
        "end_time": "2024-03-05 16:42:14"
    }
}