Dear experts,
I have been facing trouble with polarization calculation using atomate. The job starts and gets fizzled after static run of both the polar and non-polar structure. This is my python script for calculation.
from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric
import numpy as np
from pymatgen import Structure
from fireworks import LaunchPad
polar = Structure.from_file(‘BTO_polar_POSCAR’)
nonpolar = Structure.from_file(‘BTO_nonpolar_POSCAR’)
wf = get_wf_ferroelectric(polar_structure=polar, nonpolar_structure=nonpolar, vasp_cmd="/home/tddft/Code/vasp_original/bin/vasp_std", db_file=None,vasp_input_set_polar=“MPStaticSet”,vasp_input_set_nonpolar=“MPStaticSet”,relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=5, hse=False, add_analysis_task=False, wfid=None,tags=None)
lpad = LaunchPad.auto_load()
lpad.add_wf(wf)
I am getting the following error -
# (atomate_env) tddft@dft:~/Project/atomate_check/ferroelectric/BaTiO3$ python ferro.py
2019-11-09 11:52:24,953 INFO Added a workflow. id_map: {-12: 1, -10: 2, -8: 3, -6: 4, -4: 5, -2: 6}
(atomate_env) tddft@dft:~/Project/atomate_check/ferroelectric/BaTiO3$ rlaunch rapidfire
2019-11-09 11:52:37,951 INFO Hostname/IP lookup (this will take a few seconds)
2019-11-09 11:52:38,814 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:52:38,814 INFO Launching Rocket
2019-11-09 11:52:38,830 INFO RUNNING fw_id: 5 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:52:38,837 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.
2019-11-09 11:52:38,850 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}
2019-11-09 11:52:38,852 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2019-11-09 11:54:30,825 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}
2019-11-09 11:54:30,828 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.
2019-11-09 11:54:30,828 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}
2019-11-09 11:54:30,830 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.
2019-11-09 11:54:30,830 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:54:30,830 INFO atomate.vasp.drones Getting task doc for base dir :/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:54:31,499 INFO atomate.vasp.drones Post-processing dir:/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:54:31,500 WARNING atomate.vasp.drones Transformations file does not exist.
2019-11-09 11:54:31,531 INFO atomate.vasp.drones Post-processed /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063
2019-11-09 11:54:31,532 INFO Task completed: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}
2019-11-09 11:54:31,534 INFO Task started: {{atomate.vasp.firetasks.glue_tasks.CheckBandgap}}.
2019-11-09 11:54:31,534 INFO atomate.vasp.firetasks.glue_tasks Checking the gap of file: vasprun.xml.gz
2019-11-09 11:54:31,600 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.7403999999999997. Min gap: 0.01. Max gap: None
2019-11-09 11:54:31,600 INFO Task completed: {{atomate.vasp.firetasks.glue_tasks.CheckBandgap}}
2019-11-09 11:54:31,602 INFO Task started: {{atomate.common.firetasks.glue_tasks.CreateFolder}}.
2019-11-09 11:54:31,602 INFO Task completed: {{atomate.common.firetasks.glue_tasks.CreateFolder}}
2019-11-09 11:54:31,604 INFO Task started: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}.
2019-11-09 11:54:31,751 INFO Task completed: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}
2019-11-09 11:54:31,753 INFO Task started: {{atomate.vasp.firetasks.write_inputs.ModifyIncar}}.
2019-11-09 11:54:31,753 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.ModifyIncar}}
2019-11-09 11:54:31,755 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2019-11-09 11:56:23,563 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}
2019-11-09 11:56:23,565 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.
2019-11-09 11:56:23,565 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}
2019-11-09 11:56:23,567 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.
2019-11-09 11:56:23,567 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063/polarization
2019-11-09 11:56:23,567 INFO atomate.vasp.drones Getting task doc for base dir :/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063/polarization
2019-11-09 11:56:24,296 INFO atomate.vasp.drones Post-processing dir:/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063/polarization
2019-11-09 11:56:24,297 WARNING atomate.vasp.drones Transformations file does not exist.
2019-11-09 11:56:24,329 INFO atomate.vasp.drones Post-processed /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-22-38-814063/polarization
2019-11-09 11:56:24,330 INFO Task completed: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}
2019-11-09 11:56:24,357 INFO Rocket finished
2019-11-09 11:56:24,360 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:56:24,360 INFO Launching Rocket
2019-11-09 11:56:24,385 INFO RUNNING fw_id: 6 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:56:24,391 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.
2019-11-09 11:56:24,400 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}
2019-11-09 11:56:24,403 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2019-11-09 11:59:27,013 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}
2019-11-09 11:59:27,016 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.
2019-11-09 11:59:27,016 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}
2019-11-09 11:59:27,018 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.
2019-11-09 11:59:27,018 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:59:27,018 INFO atomate.vasp.drones Getting task doc for base dir :/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:59:27,754 INFO atomate.vasp.drones Post-processing dir:/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:59:27,754 WARNING atomate.vasp.drones Transformations file does not exist.
2019-11-09 11:59:27,783 INFO atomate.vasp.drones Post-processed /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342
2019-11-09 11:59:27,784 INFO Task completed: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}
2019-11-09 11:59:27,786 INFO Task started: {{atomate.vasp.firetasks.glue_tasks.CheckBandgap}}.
2019-11-09 11:59:27,786 INFO atomate.vasp.firetasks.glue_tasks Checking the gap of file: vasprun.xml.gz
2019-11-09 11:59:27,871 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.8434000000000004. Min gap: 0.01. Max gap: None
2019-11-09 11:59:27,871 INFO Task completed: {{atomate.vasp.firetasks.glue_tasks.CheckBandgap}}
2019-11-09 11:59:27,873 INFO Task started: {{atomate.common.firetasks.glue_tasks.CreateFolder}}.
2019-11-09 11:59:27,873 INFO Task completed: {{atomate.common.firetasks.glue_tasks.CreateFolder}}
2019-11-09 11:59:27,874 INFO Task started: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}.
2019-11-09 11:59:28,139 INFO Task completed: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}
2019-11-09 11:59:28,141 INFO Task started: {{atomate.vasp.firetasks.write_inputs.ModifyIncar}}.
2019-11-09 11:59:28,141 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.ModifyIncar}}
2019-11-09 11:59:28,143 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2019-11-09 12:01:20,914 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}
2019-11-09 12:01:20,917 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.
2019-11-09 12:01:20,917 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}
2019-11-09 12:01:20,920 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.
2019-11-09 12:01:20,920 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342/polarization
2019-11-09 12:01:20,920 INFO atomate.vasp.drones Getting task doc for base dir :/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342/polarization
2019-11-09 12:01:21,754 INFO atomate.vasp.drones Post-processing dir:/home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342/polarization
2019-11-09 12:01:21,754 WARNING atomate.vasp.drones Transformations file does not exist.
2019-11-09 12:01:21,786 INFO atomate.vasp.drones Post-processed /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-26-24-360342/polarization
2019-11-09 12:01:21,788 INFO Task completed: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}
2019-11-09 12:01:21,824 INFO Rocket finished
2019-11-09 12:01:21,829 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-829239
2019-11-09 12:01:21,829 INFO Launching Rocket
2019-11-09 12:01:21,842 INFO RUNNING fw_id: 1 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-829239
2019-11-09 12:01:21,846 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR}}.
Traceback (most recent call last):
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/write_inputs.py”, line 96, in run_task
structure = GetInterpolatedPOSCAR.interpolate_poscar(self, fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 263, in interpolate_poscar
name_append="_0").run_task(fw_spec=fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/firework.py”, line 70, in **init**
raise RuntimeError(“Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.”.format(self. **class** , k, allowed_params))
RuntimeError: Invalid keyword argument specified for: <class ‘atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc’>. You specified: calc_dir. Allowed values are: [‘calc_loc’, ‘filenames’, ‘name_prepend’, ‘name_append’].
2019-11-09 12:01:21,858 INFO Rocket finished
2019-11-09 12:01:21,862 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-862286
2019-11-09 12:01:21,862 INFO Launching Rocket
2019-11-09 12:01:21,877 INFO RUNNING fw_id: 2 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-862286
2019-11-09 12:01:21,880 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR}}.
Traceback (most recent call last):
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/write_inputs.py”, line 96, in run_task
structure = GetInterpolatedPOSCAR.interpolate_poscar(self, fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 263, in interpolate_poscar
name_append="_0").run_task(fw_spec=fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/firework.py”, line 70, in **init**
raise RuntimeError(“Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.”.format(self. **class** , k, allowed_params))
RuntimeError: Invalid keyword argument specified for: <class ‘atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc’>. You specified: calc_dir. Allowed values are: [‘calc_loc’, ‘filenames’, ‘name_prepend’, ‘name_append’].
2019-11-09 12:01:21,894 INFO Rocket finished
2019-11-09 12:01:21,898 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-898725
2019-11-09 12:01:21,899 INFO Launching Rocket
2019-11-09 12:01:21,912 INFO RUNNING fw_id: 3 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-898725
2019-11-09 12:01:21,916 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR}}.
Traceback (most recent call last):
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/write_inputs.py”, line 96, in run_task
structure = GetInterpolatedPOSCAR.interpolate_poscar(self, fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 263, in interpolate_poscar
name_append="_0").run_task(fw_spec=fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/firework.py”, line 70, in **init**
raise RuntimeError(“Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.”.format(self. **class** , k, allowed_params))
RuntimeError: Invalid keyword argument specified for: <class ‘atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc’>. You specified: calc_dir. Allowed values are: [‘calc_loc’, ‘filenames’, ‘name_prepend’, ‘name_append’].
2019-11-09 12:01:21,929 INFO Rocket finished
2019-11-09 12:01:21,932 INFO Created new dir /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-932771
2019-11-09 12:01:21,933 INFO Launching Rocket
2019-11-09 12:01:21,950 INFO RUNNING fw_id: 4 in directory: /home/tddft/Project/atomate_check/ferroelectric/BaTiO3/launcher_2019-11-09-06-31-21-932771
2019-11-09 12:01:21,954 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR}}.
Traceback (most recent call last):
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/write_inputs.py”, line 96, in run_task
structure = GetInterpolatedPOSCAR.interpolate_poscar(self, fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 263, in interpolate_poscar
name_append="_0").run_task(fw_spec=fw_spec)
File “/home/tddft/atomate/atomate_env/lib/python3.7/site-packages/fireworks/core/firework.py”, line 70, in **init**
raise RuntimeError(“Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.”.format(self. **class** , k, allowed_params))
RuntimeError: Invalid keyword argument specified for: <class ‘atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc’>. You specified: calc_dir. Allowed values are: [‘calc_loc’, ‘filenames’, ‘name_prepend’, ‘name_append’].
2019-11-09 12:01:21,965 INFO Rocket finished
with regards,
Bikash.