vasp_cmd array for NEB calculations?

Atomate
1

Hello,

I’m trying to run NEB calculations, but they are failing with the error

Traceback (most recent call last):
File “/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/atomate/vasp/firetasks/run_calc.py”, line 169, in run_task
ppn = int(vasp_cmd[index[0] + 1])
IndexError: list index out of range

It seems to be expecting an array of vasp_cmd, as noted recently in the comments of the code. Does anyone here know how to set the correct vasp_cmd? My current vasp_cmd is ‘ibrun tacc_affinity vasp_std’ for TACC’s Stampede 2. If I need to run the workflow in reservation mode, I’d also appreciate any advice on how to modify the .yaml files.

Thanks

2

I haven’t used the NEB workflow, and technically it shouldn’t be using a different format for VASP cmd. But since this code is from UCSD my guess is that they are using the custodian / Python subprocess-style version of command in which everything is an array:

i.e.

“'ibrun tacc_affinity vasp_std”

becomes

["'ibrun", “tacc_affinity”, “vasp_std”]

···

On Thursday, August 22, 2019 at 9:44:24 AM UTC-7, Steven Hartman wrote:

Hello,

I’m trying to run NEB calculations, but they are failing with the error

Traceback (most recent call last):
File “/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/atomate/vasp/firetasks/run_calc.py”, line 169, in run_task
ppn = int(vasp_cmd[index[0] + 1])
IndexError: list index out of range

It seems to be expecting an array of vasp_cmd, as noted recently in the comments of the code. Does anyone here know how to set the correct vasp_cmd? My current vasp_cmd is ‘ibrun tacc_affinity vasp_std’ for TACC’s Stampede 2. If I need to run the workflow in reservation mode, I’d also appreciate any advice on how to modify the .yaml files.

Thanks