Running example workflow using LAMMPS

Hi,

I just finished the installation of Atomate and I was able to successfully configuring FireWorks. I was also able to made sure that I could successfully connect to the MongoDB by running the lpad reset command.

I would like now to run a simple workflow test but the only documentation I can find on the website is using VASP.

I was wondering if anyone have any simple LAMMPS test workflow that I can run.

Thank you

Alessandro

Hi Alessandro,

The original developer of the LAMMPs module is no longer maintaining it, and the underlying pymatgen library has changed significantly in the meantime so the existing LAMMPs workflows in atomate will not function correctly.

There are plans to revive the LAMMPs functionality in atomate in the future:

https://github.com/hackingmaterials/atomate/issues/245

At that point, we will also try to improve the documentation.

Unfortunately, there is no set time line for this so I’m not sure when it will be completed.

···

On Friday, June 1, 2018 at 1:32:46 PM UTC-7, [email protected] wrote:

Hi,

I just finished the installation of Atomate and I was able to successfully configuring FireWorks. I was also able to made sure that I could successfully connect to the MongoDB by running the lpad reset command.

I would like now to run a simple workflow test but the only documentation I can find on the website is using VASP.

I was wondering if anyone have any simple LAMMPS test workflow that I can run.

Thank you

Alessandro

Anubhav,

Thank you for the reply, it is unfurtunate that the LAMMPS part of the project is not longer under maintenance. However I was able to modify the python script in order to create a basic workflow using lammps and also to initiate the launchpad and add the workflow to it.

The script ran successfully and the workflow was added to the launchpad correctly and i was able to see it by running the command “lpad get_flows”

However once I tried to submit it using the “qlaunch rapidfire” command I am always get the same error

Traceback (most recent call last):

File “/home/aperego/anaconda3/bin/qlaunch”, line 11, in

sys.exit(qlaunch())

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 203, in qlaunch

do_launch(args)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 52, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 384, in load_object_from_file

f_format = filename.split(’.’)[-1]

AttributeError: ‘NoneType’ object has no attribute ‘split’

This happens if run the command in the same directory were my input file and workflow script are.

If i change my directory to the atomate/config directory and run the “qlaunch rapdifire” command i am getting this error:

Traceback (most recent call last):

File “/home/aperego/anaconda3/bin/qlaunch”, line 11, in

sys.exit(qlaunch())

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 203, in qlaunch

do_launch(args)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 48, in do_launch

args.launchpad_file) if args.launchpad_file else LaunchPad(

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 286, in from_file

return cls.from_format(f.read(), f_format=f_format)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 254, in from_format

yaml.safe_load(f_str)))

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 221, in from_dict

ssl_ca_certs, ssl_certfile, ssl_keyfile, ssl_pem_passphrase)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 152, in init

self.db.authenticate(username, password)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/database.py”, line 1167, in authenticate

connect=True)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 583, in _cache_credentials

writable_preferred_server_selector)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 224, in select_server

address))

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 183, in select_servers

selector, server_timeout, address)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 199, in _select_servers_loop

self._error_message(selector))

pymongo.errors.ServerSelectionTimeoutError: homer3:27017: [Errno 111] Connection

Same thing happen if I run the "singleshot command.

So I don’t know if this is related to the pymatgen library as you motioned or I have some other underlying issues with my database connection. I’ll keep looking into I and maybe I will be able to make it work.

Thank you for you answers

Alessandro

···

On Mon, Jun 11, 2018 at 10:34 AM, Anubhav Jain [email protected] wrote:

Hi Alessandro,

The original developer of the LAMMPs module is no longer maintaining it, and the underlying pymatgen library has changed significantly in the meantime so the existing LAMMPs workflows in atomate will not function correctly.

There are plans to revive the LAMMPs functionality in atomate in the future:

https://github.com/hackingmaterials/atomate/issues/245

At that point, we will also try to improve the documentation.

Unfortunately, there is no set time line for this so I’m not sure when it will be completed.

On Friday, June 1, 2018 at 1:32:46 PM UTC-7, [email protected] wrote:

Hi,

I just finished the installation of Atomate and I was able to successfully configuring FireWorks. I was also able to made sure that I could successfully connect to the MongoDB by running the lpad reset command.

I would like now to run a simple workflow test but the only documentation I can find on the website is using VASP.

I was wondering if anyone have any simple LAMMPS test workflow that I can run.

Thank you

Alessandro

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Hi Alessandro,

Regarding LAMMPs, I think the MAVRL (Ong) group at UC San Diego plans to build out the feature in atomate as per the issue. But I am not sure when exactly they will do this. Shyue Ping Ong has said they are quite interested in this. You might have your research group reach out to his to coordinate if this sounds useful.

As for the specific error, what happens if you type “qlaunch -q <PATH/TO/YOUR/MY_QADAPTER.YAML> rapidfire”

(with the part in brackets replaced by the path to your queue adapter file)

From what I can tell the problem looks related to finding the correct “my_qadapter.yaml” file.

Anubhav

···

On Tue, Jun 12, 2018 at 10:42 AM, Alessandro Perego [email protected] wrote:

Anubhav,

Thank you for the reply, it is unfurtunate that the LAMMPS part of the project is not longer under maintenance. However I was able to modify the python script in order to create a basic workflow using lammps and also to initiate the launchpad and add the workflow to it.

The script ran successfully and the workflow was added to the launchpad correctly and i was able to see it by running the command “lpad get_flows”

However once I tried to submit it using the “qlaunch rapidfire” command I am always get the same error

Traceback (most recent call last):

File “/home/aperego/anaconda3/bin/qlaunch”, line 11, in

sys.exit(qlaunch())

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 203, in qlaunch

do_launch(args)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 52, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 384, in load_object_from_file

f_format = filename.split(’.’)[-1]

AttributeError: ‘NoneType’ object has no attribute ‘split’

This happens if run the command in the same directory were my input file and workflow script are.

If i change my directory to the atomate/config directory and run the “qlaunch rapdifire” command i am getting this error:

Traceback (most recent call last):

File “/home/aperego/anaconda3/bin/qlaunch”, line 11, in

sys.exit(qlaunch())

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 203, in qlaunch

do_launch(args)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/scripts/qlaunch_run.py”, line 48, in do_launch

args.launchpad_file) if args.launchpad_file else LaunchPad(

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 286, in from_file

return cls.from_format(f.read(), f_format=f_format)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/utilities/fw_serializers.py”, line 254, in from_format

yaml.safe_load(f_str)))

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 221, in from_dict

ssl_ca_certs, ssl_certfile, ssl_keyfile, ssl_pem_passphrase)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/fireworks/core/launchpad.py”, line 152, in init

self.db.authenticate(username, password)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/database.py”, line 1167, in authenticate

connect=True)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/mongo_client.py”, line 583, in _cache_credentials

writable_preferred_server_selector)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 224, in select_server

address))

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 183, in select_servers

selector, server_timeout, address)

File “/home/aperego/anaconda3/lib/python3.6/site-packages/pymongo/topology.py”, line 199, in _select_servers_loop

self._error_message(selector))

pymongo.errors.ServerSelectionTimeoutError: homer3:27017: [Errno 111] Connection

Same thing happen if I run the "singleshot command.

So I don’t know if this is related to the pymatgen library as you motioned or I have some other underlying issues with my database connection. I’ll keep looking into I and maybe I will be able to make it work.

Thank you for you answers

Alessandro

On Mon, Jun 11, 2018 at 10:34 AM, Anubhav Jain [email protected] wrote:

Hi Alessandro,

The original developer of the LAMMPs module is no longer maintaining it, and the underlying pymatgen library has changed significantly in the meantime so the existing LAMMPs workflows in atomate will not function correctly.

There are plans to revive the LAMMPs functionality in atomate in the future:

https://github.com/hackingmaterials/atomate/issues/245

At that point, we will also try to improve the documentation.

Unfortunately, there is no set time line for this so I’m not sure when it will be completed.

On Friday, June 1, 2018 at 1:32:46 PM UTC-7, [email protected] wrote:

Hi,

I just finished the installation of Atomate and I was able to successfully configuring FireWorks. I was also able to made sure that I could successfully connect to the MongoDB by running the lpad reset command.

I would like now to run a simple workflow test but the only documentation I can find on the website is using VASP.

I was wondering if anyone have any simple LAMMPS test workflow that I can run.

Thank you

Alessandro

You received this message because you are subscribed to a topic in the Google Groups “atomate” group.

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To post to this group, send email to [email protected].

To view this discussion on the web visit https://groups.google.com/d/msgid/atomate/823f4d67-d72d-4974-8111-b7bb4fff6700%40googlegroups.com.

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