Open sradl1981 opened 7 years ago
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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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
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
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okey, but
soft-register-entity chemkinreaction.json and re-running remarc-wrapper and genudf.js
has zero errect.
there is no obvious documentation that explains the syntax of the registration tool, or automates this.
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).
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).
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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).**
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 ==