Hi,
I'm trying to perform a very simple vasp simulation with Fireworks in nersc#cori machine. However it throws me an error that I'm unable to resolve. The details are as follows
0. The fireworks, fireworks-vasp, pymatgen and custodian was installed in a local python virtual environment from sourcecode.
1
. Structure: Ba atom in a cubic cell of length 10Angstrom (input file POSCAR_Ba is attached)
2.
Yaml File: The python code to create the yaml file is as follows (The output VAPS_Ba.yaml is attached)
from fireworks import Firework
from fireworks_vasp.tasks import WriteVaspInputTask, VaspCustodianTask, VaspAnalyzeTask
from pymatgen.core.structure import Structure
def create_fireworks(structure, keyVal, viset='MPVaspInputSet', params={}, handlers="all", vasp_cmd=["srun","-n","128","/usr/common/software/vasp/5.4.1/hsw/bin/vasp_std"]):
name = structure.formula
wf_name = name
t1 = WriteVaspInputTask(structure=structure, vasp_input_set=viset, input_set_params=params)
t2 = VaspCustodianTask(vasp_cmd=vasp_cmd, handlers=handlers)
t3 = VaspAnalyzeTask()
workflow = Firework([t1, t2, t3], name=name)
return workflow
if __name__ == '__main__':
inFileName = 'POSCAR_Ba'
crystalStruc = Structure.from_file(inFileName)
keyVal = 'Ba-Atom'
workflow = create_fireworks(crystalStruc,keyVal)
workflow.to_file("VASP_Ba.yaml")
3. The yaml file is added to workflow with command
4. When I run the fireworks with command qlaunch fireworks, I get the following error
Traceback (most recent call last):
File "/global/u1/r/rbala/pythonVirtualEnvs/pymatgenCori_Python2
_7_9_Nov2015/lib/python2.7/site-packages/FireWorks-1.2.1-py2.7.eg
g/fireworks/core/rocket.py", line 211, in run
m_action = t.run_task(my_spec)
File "/global/u1/r/rbala/pythonVirtualEnvs/pymatgenCori_Python2
_7_9_Nov2015/lib/python2.7/site-packages/fireworks_vasp-0.2-py2.7
.egg/fireworks_vasp/tasks.py", line 45, in run_task
s = Structure.from_dict(self["structure"])
File "/global/u1/r/rbala/pythonVirtualEnvs/pymatgenCori_Python2
_7_9_Nov2015/lib/python2.7/site-packages/pymatgen-3.2.7-py2.7-lin
ux-x86_64.egg/pymatgen/core/structure.py", line 1246, in from_dic
t
lattice = Lattice.from_dict(d["lattice"])
File "/global/u1/r/rbala/pythonVirtualEnvs/pymatgenCori_Python2
_7_9_Nov2015/lib/python2.7/site-packages/pymatgen-3.2.7-py2.7-lin
ux-x86_64.egg/pymatgen/core/structure.py", line 190, in __getitem
__
return self.sites[ind]
TypeError: list indices must be integers, not unicode
Thank you,
Best
Ram