Skip to content

Latest commit

 

History

History
78 lines (50 loc) · 2.45 KB

README.md

File metadata and controls

78 lines (50 loc) · 2.45 KB
Raw

Reflectometry Database

A mongodb database containing parameters for materials used in reflectometry, and their reflectivity parameters. The values used to create informed and uniform priors are included for the relevant parameters. The following parameters are currently included (with the italic parameters having prior values available):

Molecular parameters:

  • CAS number
  • Molecular volume
  • Molecular weight
  • Molecular scattering length density
  • Area per molecule

Amphiphile parameters:

  • Head volume
  • Tail volume
  • Head scattering length
  • Tail scattering length

Phospholipid parameters:

  • Natural or synthetic?

Reflectivity parameters:

  • Tail thickness
  • Head thickness
  • Roughness
  • phi_h (check what this is?)
  • phi_t (check what this is?)

Examples of using the database:

To build the database, type in the terminal (not a mongo shell):

cd refl-database-main

mongorestore --db refl_database db/dump/refl_database

To check whether the collections were imported successfully:

mongo

show dbs

use refl_database

show collections

To show the entries in a collection, for example in the amphiphiles collection:

db.amphiphiles.find({})

To show how many entries there are in a collection, e.g. how many phospholipids there are:

db.phospholipids.count()

To get all of the parameters for a single molecule, such as DMPC:

db.getCollection('molecules').aggregate([

{$match : {name : "DMPC"}},

{$lookup: {from: "amphiphiles",localField: "name",foreignField: "name",as: "amphiphiles"}}, 
{$unwind:"$amphiphiles"},
{$project:{"amphiphiles.name":0,"amphiphiles.cas_no":0,"amphiphiles._id":0}}, 

{$lookup: {from: "phospholipids", localField: "name", foreignField: "name", as:"phospholipids"}},
{$unwind:"$phospholipids"}, 
{$project:{"phospholipids.name":0,"phospholipids.cas_no":0,"phospholipids._id":0}}, 

{$lookup: {from: "reflectivity_parameters", localField: "name", foreignField: "name", as: "reflectivity_parameters"}}, 
{$unwind: "$reflectivity_parameters"}, 
{$project:{"reflectivity_parameters.name":0,"reflectivity_parameters.cas_no":0,"reflectivity_parameters._id":0}}

]).pretty()

To find the values to use for priors for a parameter, e.g. the head volume for DMPC:

db.Gaussian.find({"name":"DMPC","parameter":"v_h"},{"_id":0,"name":0,"parameter":0}).pretty()