remarc-wrapper (or what ever this should be) does not save chemkin reaction in database

[sradl1981]

when running

~/NanoSim/run-soft5/examples/remarc/rmc-vasp.sh

it appears that everything runs fine (so SurfaceChemkin.inp and Chemkin.inp is produced), the the following step to produce the udf (i.e., ~/NanoSim/run-soft5/examples/udfgen/genudf.js) produces

sradl@Corellia:~/NanoSim/run-soft5/examples/udfgen> ./genudf.js {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4} [ERROR] cannot find entity chemkinReaction:0.1 in database == STACKTRACE ==

(err = '[ERROR] cannot find entity chemkinReaction:0.1 in database') at /usr/local/soft5/lib64/soft5/modules/porto/entity.js:10 (entityName = 'chemkinReaction', entityNamespace = 'eu.nanosim.vasp', entityVersion = '0.1', callback = function (err) { if (err) throw (err); }) at /usr/local/soft5/lib64/soft5/modules/porto/factory.js:21 (entityName = 'chemkinReaction', entityNamespace = 'eu.nanosim.vasp', entityVersion = '0.1') at /usr/local/soft5/lib64/soft5/modules/porto/entity.js:11 () at ./genudf.js:4 In: ./genudf.js Application arguments: softshell ./genudf.js {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4} This is a problem

[quaat]

Hi Yes this is indeed a mistake as thr documentation should state that the entity should first be published (registered) in the metadata-database. you find the json file in the folder porto/src/entities and register it by using the register-entity command.

Best Thomas

On Oct 3, 2017 12:01 PM, "Stefan Radl" notifications@github.com wrote:

when running

~/NanoSim/run-soft5/examples/remarc/rmc-vasp.sh

it appears that everything runs fine (so SurfaceChemkin.inp and Chemkin.inp is produced), the the following step to produce the udf (i.e., ~/NanoSim/run-soft5/examples/udfgen/genudf.js) produces

sradl@Corellia:~/NanoSim/run-soft5/examples/udfgen> ./genudf.js {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4} [ERROR] cannot find entity chemkinReaction:0.1 in database == STACKTRACE == (err = '[ERROR] cannot find entity chemkinReaction:0.1 in database') at /usr/local/soft5/lib64/soft5/modules/porto/entity.js:10 (entityName = 'chemkinReaction', entityNamespace = 'eu.nanosim.vasp', entityVersion = '0.1', callback = function (err) { if (err) throw (err); }) at /usr/local/soft5/lib64/soft5/modules/porto/factory.js:21 (entityName = 'chemkinReaction', entityNamespace = 'eu.nanosim.vasp', entityVersion = '0.1') at /usr/local/soft5/lib64/soft5/ modules/porto/entity.js:11 () at ./genudf.js:4 In: ./genudf.js Application arguments: softshell ./genudf.js {70fee6db-9bb5-472d-b0e4- 85aae0d6a6b4}

This is a problem

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[sradl1981]

No, moving to

/home/sradl/NanoSim/soft5/porto/src/entities

issuing

soft-register-entity *

and re-running

remarc-wrapper . {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4}

./genudf.js {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4}

has zero effect

[quaat]

Wildcard does not work

On Oct 3, 2017 12:23 PM, "Stefan Radl" notifications@github.com wrote:

No, moving to

/home/sradl/NanoSim/soft5/porto/src/entities

issuing

soft-register-entity *

and re-running

remarc-wrapper . {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4}

./genudf.js {70fee6db-9bb5-472d-b0e4-85aae0d6a6b4}

has zero effect

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NanoSim/Porto/issues/11#issuecomment-333801005, or mute the thread https://github.com/notifications/unsubscribe-auth/AAi_6Qp01D18SUKKkfs2dyuY95uv6P3Gks5sogsNgaJpZM4Pr3k6 .

[sradl1981]

okey, but

soft-register-entity chemkinreaction.json and re-running remarc-wrapper and genudf.js

has zero errect.

[sradl1981]

there is no obvious documentation that explains the syntax of the registration tool, or automates this.

[sradl1981]

The script remarc/vasp_data.py

issues a warning: remarc/vasp_data.py:24: UserWarning: SOFT is not available

I assume this should be an error (i.e., the case will not continue normally).

[quaat]

I think this is an internal non-issue of remarc, and can be safely ignored. I will forward this to Jesper and Stefan A to verify this.

On Oct 4, 2017 10:18 PM, "Stefan Radl" notifications@github.com wrote:

The script remarc/vasp_data.py

issues a warning: remarc/vasp_data.py:24: UserWarning: SOFT is not available

I assume this should be an error (i.e., the case will not continue normally).

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NanoSim/Porto/issues/11#issuecomment-334276878, or mute the thread https://github.com/notifications/unsubscribe-auth/AAi_6SsDehgfaX8FuEFey8OziYp8Uzlfks5so-gqgaJpZM4Pr3k6 .

[sradl1981]

The problem is: the entity names do not match, and entities appear not be auto-registered

The entity is here: https://github.com/NanoSim/Porto/blob/porto/Preview-Final-Release/porto/examples/entities/eu.nanosim.vasp.chemkin_reaction.json#L2

but the entities are called differently here https://github.com/NanoSim/Porto/blob/porto/Preview-Final-Release/porto/examples/udfgen/genudf.js#L5 https://github.com/NanoSim/Porto/blob/porto/Preview-Final-Release/porto/examples/chemkin_generator/inspectChemkinReactionEntity.js#L4 https://github.com/NanoSim/Porto/blob/porto/Preview-Final-Release/porto/examples/chemkin_generator/chemkinReactionEntity-to-chemkinFile.js#L4

Even more, there is a triplication of entities!

**Decision: we will stick with entities here https://github.com/NanoSim/Porto/tree/porto/Preview-Final-Release/porto/src/entities

and remove all unused (and duplicates, e.g., in example/entities).**