dflow101_electronic structure calculation_VASP_pymatgen

[veritas496]

To Whom It May Concern,

Please find the enclosed link for my dflow proposal.

This project is for electronic structure calculation. Traditionally, this kind of calculation tasks is repeated and requires similar calculation files. In other words, in most case we just need to modify corresponding parameters in INCAR. This structured workflow means it can be achieved automatically. With the aid of dflow, we can use all kinds of python package to finish our task. In this work, pymatgen was used to obtain structure information, write cif file, generate calculation files for opt, read INCAR parameters, modify INCAR parameters, and submit tasks in parallel.

This dflow proposal seems simple but definitely can be used further, especially in high throughput calculation.

Please feel free to give your any suggestion and comments.

Best Regards,
Yani
PhD student

[likefallwind]

Please copy your readme info here

[veritas496]

dflow: electronic structure calculation based on VASP and pymatgen

Introduction

This dflow proposal is for electronic structure calculations using VASP, from obtaining cif structure information to structure optimization, and then to calculate several electronic structure properties in parallel, ELF and charge density as examples in this project.

Details

Traditional workflow

Traditionally, we need to obtain the .cif file containing structure information from some database, e.g. Material Project, and then prepare calculation files required for VASP calculation. After that, it is the time to submit a structure optimization task and then with optimized structure, we need to modify parameters in INCAR and then submit a calculation task for ELF, and then modify parameters in INCAR to submit another calculation task for charge density.

New workflow based on dflow

However, with the aid of dflow, the workflow can be achieve automatically. The dflow workflow diagram is shown in Figure 1.

Figure 1. The dflow diagram for electronic calculation based VASP

Codes

OP

1. Obtain CIF file from Material Project

• input:

  • api-key (if you have no ideas about api-key, please refer to this website)
  • mp-id: it is the material ID in Material Project. Each material has its own material ID in Material Project.

• output:

  • CIF file

• execute:

  • MPRester: using this pymatgen module, we can access to Material project by API.
  • CifWriter: this pymatgen module helps to obtain structure information and then write a .cif file.

class DownloadCIF(OP):
    def __init__(self):
        pass

    @classmethod
    def get_input_sign(cls):
        return OPIOSign({
            'api-key' : str,
            'mp-id'  : int,
        })

    @classmethod
    def get_output_sign(cls):
        return OPIOSign({
            'DownloadCIF_output' : Artifact(Path),
        })

    @OP.exec_sign_check
    def execute(self, op_in : OPIO):
        from pymatgen.ext.matproj import MPRester
        from pymatgen.io.cif import CifWriter
        api_key=op_in['api-key']
        mp_id=str(op_in['mp-id'])
        mpr=MPRester(str(api_key))
        structure=mpr.get_structure_by_material_id(f'mp-{mp_id}',final=True,conventional_unit_cell=True)
        CifWriter(structure).write_file(f'{mp_id}.cif')

        return OPIO({
            "DownloadCIF_output": Path(f'{mp_id}.cif')
        })

2. Prepare VASP structure optimization files

• execute:
  • Structure: this pymatgen module can read cif file and then get structure information
  • MPRelaxSet: it can generate VASP calculation files for structure optimizaion automatically

class VASPPrep(OP):
    def __init__(self):
        pass
    
    @classmethod
    def get_input_sign(cls):
        return OPIOSign({
            'VaspPre_input': Artifact(Path)
        })

    @classmethod
    def get_output_sign(cls):
        return OPIOSign({
            'VaspPre_output': Artifact(Path)
        })
    
    @OP.exec_sign_check
    def execute(self, op_in: OPIO) -> OPIO:
        from pymatgen.core import Structure
        from pymatgen.io.vasp.sets import MPRelaxSet, MITRelaxSet
        structureOpt = Structure.from_file(filename=op_in['VaspPre_input'])
        relax_set = MPRelaxSet(structure=structureOpt)
        # relax_set = MITRelaxSet(structure=optStructure)#MPRelaxSet(structure=optStructure)
        relax_set.write_input(output_dir="VaspOpt")

        return OPIO({"VaspPre_output" : Path('./VaspOpt')})

3. VASP structure optimization calculation

• input:

  • VaspOpt_input: this artifact contains all required files for structure optimization based on VASP
  • running_cores: by this parameter, you can set the number of cores to be used for this calculation

• execute:

  • you are supposed to set your own VASP execute in the command here

class VASPOpt(OP):
    def __init__(self):
        pass

    @classmethod
    def get_input_sign(cls):
        return OPIOSign({
            "VaspOpt_input": Artifact(Path),
            "running_cores": int
        })

    @classmethod
    def get_output_sign(cls):
        return OPIOSign({
            "VaspOpt_output": Artifact(Path)
        })

    @OP.exec_sign_check
    def execute(self, op_in: OPIO) -> OPIO:
        cwd = os.getcwd()
        os.chdir(op_in["VaspOpt_input"])    
        cmd = f'source /public1/soft/intel/2020/parallel_studio_xe_2020/psxevars.sh &&\
                mpirun -np {str(op_in["running_cores"])} /your-VASP-execute-environment/bin/vasp_vtst_std'
        subprocess.call(cmd, shell=True)
        os.chdir(cwd)        
        return OPIO({
            "VaspOpt_output": Path(op_in["VaspOpt_input"])/"CONTCAR",
        })

4. Electronic structure calculation (ELF, charge density)

• execute:
  • inputs: this module can read parameters in INCAR as dictionary and modify/add parameters easily.

class VASPSingle(OP):
    def __init__(self):
        pass

    @classmethod
    def get_input_sign(cls):
        return OPIOSign({
            "VaspSingle_input_optModel": Artifact(Path),
            "VaspSingle_input": Artifact(Path),
            "running_cores": int,
            "INCARfromOpt": dict,
            "AIMCAR": str
        })

    @classmethod
    def get_output_sign(cls):
        return OPIOSign({
            "VaspSingle_output": Artifact(Path)  
        })

    @OP.exec_sign_check
    def execute(self, op_in: OPIO) -> OPIO:
        cwd = os.getcwd()
        os.system(f'mv {op_in["VaspSingle_input_optModel"]}/CONTCAR {op_in["VaspSingle_input"]}/POSCAR')
        os.chdir(op_in["VaspSingle_input"])
        from pymatgen.io.vasp import inputs
        incar_opt = inputs.Incar().from_file("INCAR")
        for key, value in op_in["INCARfromOpt"].items():
            incar_opt[key] = value
        incar_opt.write_file("INCAR")
        cmd = f'source /public1/soft/intel/2020/parallel_studio_xe_2020/psxevars.sh &&\
                mpirun -np {str(op_in["running_cores"])} /your-VASP-execute-environment/bin/vasp_vtst_std'
        subprocess.call(cmd, shell=True)
        os.chdir(cwd)  
        return OPIO({
            "VaspSingle_output": Path(op_in["VaspSingle_input"])/op_in["AIMCAR"], 
        })

Slurm connection

You are expected to enter your slurm information in this part, e.g. host, port, username, password, and header.

def slurm_exe(cores: int):
    """
    you are expected to enter your slurm information in this part, e.g. host, port, username, password, and header.
    """

    slurm_remote_executor = SlurmRemoteExecutor(
    host="your host",
    port=22,
    username="your username",
    password="your password", 
    header=f"#!/bin/bash\n#SBATCH --nodes=1\n#SBATCH --ntasks-per-node={str(cores)}\n#SBATCH --partition=xxx\n#SBATCH -e output.err", 
    )
    return slurm_remote_executor

add step

You are expected to enter your Material Project API key and targeted model's ID. For example, mp-id=30 is for Cu.

def main():
    """
    you are expected to enter your Material Project API key and targeted model's ID. For example, mp-id=30 is for Cu.
    """
    Download_CIF = Step(
        "download-cif",
        PythonOPTemplate(DownloadCIF, image="kianpu/pymatgen"),
        parameters={"api-key":"your api-key","mp-id":30},
    )

    VASP_prep = Step(
        "vasp-prep",
        PythonOPTemplate(VASPPrep,command=["source ~/.start_miniconda.sh && conda activate my_pymatgen && python"]),
        artifacts={"VaspPre_input":Download_CIF.outputs.artifacts["DownloadCIF_output"]},
        executor=slurm_exe(1),
    )

    Structure_Opt = Step(
        "structure-opt",
        PythonOPTemplate(VASPOpt,command=["source ~/.start_miniconda.sh && conda activate my_pymatgen && python"]),
        artifacts={"VaspOpt_input": VASP_prep.outputs.artifacts["VaspPre_output"]},
        parameters={"running_cores": 64},
        executor=slurm_exe(128),
    )

    Single_elf = Step(
        "single-elf",
        PythonOPTemplate(VASPSingle, command=["source ~/.start_miniconda.sh && conda activate my_pymatgen && python"]),
        artifacts={
            "VaspSingle_input_optModel": Structure_Opt.outputs.artifacts["VaspOpt_output"],
            "VaspSingle_input": VASP_prep.outputs.artifacts["VaspPre_output"]
            }, 
        parameters={
            "running_cores":64,
            "INCARfromOpt": {"LELF": ".TRUE."},
            "AIMCAR": "ELFCAR",
        },
        executor=slurm_exe(128),
    )

    Single_density = Step(
        "single-density",
        PythonOPTemplate(VASPSingle, command=["source ~/.start_miniconda.sh && conda activate my_pymatgen && python"]),
        artifacts={
            "VaspSingle_input_optModel": Structure_Opt.outputs.artifacts["VaspOpt_output"],
            "VaspSingle_input": VASP_prep.outputs.artifacts["VaspPre_output"]
            }, 
        parameters={
            "running_cores":64,
            "INCARfromOpt": {"LCHARG":".TRUE.", "NSW": 0},
            "AIMCAR": "CHGCAR",
        },
        executor=slurm_exe(128),
    )

    wf = Workflow(name="vasp-task")
    wf.add(Download_CIF)
    wf.add(VASP_prep)
    wf.add(Structure_Opt)
    wf.add([Single_elf, Single_density])
    wf.submit()

if __name__ == "__main__":
    main()

[likefallwind]

ok please make a pr