Initial project version
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.gitignore
vendored
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.gitignore
vendored
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data/
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__pycache__
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*.pyc
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store.egg-info/
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build/
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dist/
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.idea/
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.cache/
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244
README.md
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README.md
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# Store.py: A database interface for storing MD evaluation data
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A database interface to store evaluations of MD simulations.
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## Usage
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The package provides interfaces to query records from the database (`get()` function)
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and put new or updated records into the database (`update()` function).
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Both of which will be explained breifly below.
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### Automated Evaluation: `eval.yaml`
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The package provides a standardized way of running MD evaluations.
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Those evaluations are defined in `eval.yaml` file, located in the respective simulation directory.
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An example format of such a yaml file is as follows:
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namespace: analyse.biwater
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simulation_params:
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mixingratio: 0.5
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system: bulk
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ensemble: nvt
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trajectory-open: open
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evaluations:
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- subset:
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residue_name: W100
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atom_name: OW
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selection: W100
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functions:
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- isf:
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q: 22.7
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- msd
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- subset:
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residue_name: W100
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atom_name: OW
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selection: W100
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other:
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residue_name: W075
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atom_name: OW
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selection: W075
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functions:
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- rdf
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- subset:
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residue_name: W100
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coordinates-map: water_dipole
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selection: dipole
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functions:
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- oaf:
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order: 1
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The first line defines a namespace, which is used to locate evaluation functions (see below).
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The key `simulation_params` defines parameters of the simulation, which are used when storing the results in the database.
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Parameters like the directory and the user are determined automatically from the file path and the current user, respectively.
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With the key `trajectory-open` a function can be specified that is used to open the trajectory.
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If this is omitted the function store.eval.open will be used.
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The last key `evaluations` defines a list of evaluations which will be done.
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Each item of the list is a dictionary with the two keys `subset` and und `functions`.
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The parameters defined for the subset will be used to get the subset of the trajectory ,except for the special key `selection` which is used for the store.update function.
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The optional key `other` defines a second subset of atoms, which is passed to the function as the keyword other.
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The functions are again defined as a list. Each item can be either a string or a dictionary with on key value pair.
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In the latter case the key defines the function and the value should be another dictionary of keyword arguments for the function.
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These keyword arguments will also be stored in the database, as evaluation parameters.
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The function is located by its name, first in the specified namespace and if not found there, in the store.analyse module, which defines some standard MD evaluation functions.
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The namespace may be used to calculate user defined functions.
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The above example doese the following evaluations:
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1. All results will be stored in the database with the parameters system=bulk, ensemble=nvt, mixingratio=0.5.
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2. The trajectory will be opened with the function analyse.biwater.open and the path of the yaml file.
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3. The first subset selects all OW atoms of the W100 residues, the selection parameter in the database will be W100.
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4. The first function will either be analyse.biwater.isf (if existent) or store.analyse.isf, with the keyword argument q=22.7.
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5. The second functions msd has no arguments.
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6. A second subset selects all atoms of the W100 residue and runs the functions F1 and F2 with it.
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### Included analysis functions
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The store package comes with some basic analysis functions, which can also serve as template for writing customized analyses.
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All analysis functions are defind in `store.analyse`, this is also the fall back namespace for eval.yaml evaluations,
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when no namespace is specified, or functions are not defined in the custom namespace.
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Currently, the following functions are defined, some of them are documented, use help(store.analyse.function) to get more info.
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The follwoing list gives the names and required parameters (in parantheses) of the avaliable functions:
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- isf(q): Incoherent intermediate scatterig function
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- csf(q): Coherent intermediate scattering function
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- msd: Mean squared displacement
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- oaf(order): Orientational autocorrelation function, use with appropriate vector map (see below)
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- rdf: Radial pair distribution function
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- tetrahedral_order: Tetrahedral oder parameter
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Additionally, some typical vector maps are defined:
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- vector: Generic vector map between two atom types
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- water_dipole
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- water_OH_bonds
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### Updating
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The function `update` handles creation of new records as updating existing ones.
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It will look for a simulation in the database, according to the specified arguments
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and only if no matching record is found, a new simulation will be created.
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import store
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store.update(
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'isf', df, directory='/path/to/simulation', user='niels', T=120, selection='OW',
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simulation_params={'mixingratio': 0.5}, evaluation_params={'q': 22.7}
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)
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Here the variable `df` should be a dataframe with the evaluated data.
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### Querying
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Users should use the function `get` to retrieve data from the database. For example:
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import store
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store.get(
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'isf', user='niels', T='100-150',
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simulation_params={'mixingratio': 0.5}
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)
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Note that the parameters defined as `simulation_params` (or `evaluation_params`) have
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to be defined when the data is put into the database.
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## Database organization
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The database is organized in two main Tables:
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1. Evaluation: Stores the evaluated data, linked to a simulation
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2. Simulation: Stores the metadata of a simulation
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### Table schemas
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Evaluation:
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observable: str
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selection: str
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parameters: list of Parameter
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simulation: Simulation
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data: object
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Simulation:
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directory: str
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user: str
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temperature: number
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float_params: list of FloatAttribute
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string_params: list of StringAttribute
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evaluations: list of Evaluation
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Parameter:
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name: str
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value: float
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FloatAttribute:
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name: str
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value: float
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StringAttribute:
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name: str
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value: str
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The tables Parameter, FloatAttribute and StringAttribute are simple key values pairs,
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allowing float or string values, respectively. They are used to store arbitrary
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attributes of the evaluation and simualtion records.
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## Notes for the future
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### Clean-Up SQL Database
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To delete orphaned evaluations, on the postgresql shell (`psql -h db.cluster -U store`)
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# Since parameters refernce their respective evaluation, we have to delete them first.
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DELETE FROM parameters
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WHERE parameters.evaluation_id IN
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(SELECT id FROM evaluations WHERE evaluations.simulation_id IS NULL);
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DELETE FROM evaluations WHERE evaluations.simulation_id IS NULL;
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Similarly, one can delete simulations, without any assigned evaluations.
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### Database usages
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General size info
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SELECT nspname || '.' || relname AS "relation",
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pg_size_pretty(pg_total_relation_size(C.oid)) AS "total_size"
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FROM pg_class C
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LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
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WHERE nspname NOT IN ('pg_catalog', 'information_schema')
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AND C.relkind <> 'i'
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AND nspname !~ '^pg_toast'
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ORDER BY pg_total_relation_size(C.oid) DESC
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LIMIT 20;
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Number of simulations per User
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SELECT simulations.user, COUNT(DISTINCT simulations),
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pg_size_pretty(SUM(pg_column_size(data))) as "data-size",
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pg_size_pretty(SUM(pg_column_size(data)) / COUNT(DISTINCT simulations)) as "size / sim"
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FROM evaluations
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JOIN simulations
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ON (simulations.id = evaluations.simulation_id)
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GROUP BY simulations.user
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ORDER BY count DESC;
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Average size of data per observable
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SELECT observable,
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pg_size_pretty(ROUND(AVG(pg_column_size(data)), 0)) as "size-avg",
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pg_size_pretty(ROUND(SUM(pg_column_size(data)), 0)) as "size-total",
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AVG(pg_column_size(data)) as "size_bytes"
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FROM evaluations
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GROUP BY observable
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ORDER BY size_bytes DESC;
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### SSH tunnel connection
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To get a secure connection to the postgrsql server an nas2, one can use SSH tunnels.
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This allows to use SSH certicifates for identification, so no passwords are reuqired.
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Example code fragments:
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import sshtunnel
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ssh_server = None
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SSH_HOST = 'nas2'
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SSH_USER = os.getlogin()
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SSH_KEY = os.environ['HOME'] + '/.ssh/id_rsa'
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SSH_BIND_PORT = 58222
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DB_FILE = 'postgresql://localhost:{port}/test'.format(port=SSH_BIND_PORT)
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def open_sshtunnel():
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global ssh_server
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ssh_server = sshtunnel.SSHTunnelForwarder(
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ssh_address_or_host=SSH_HOST,
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ssh_username=SSH_USER,
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ssh_pkey=SSH_KEY,
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remote_bind_address=('localhost', PG_PORT),
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local_bind_address=('localhost', SSH_BIND_PORT)
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)
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ssh_server.start()
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debug.cfg
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debug.cfg
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[store]
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db_file = sqlite:////home/phd/Dokumente/store.db
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[eval]
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require_trajectory = True
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maxcache = 1024
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topology = *.tpr
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trajectory = out/*.xtc
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short_dir = ../short/*
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nojump = True
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[correlation]
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skip = 0.01
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window = 0.3
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segments = 300
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setup.py
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setup.py
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from setuptools import setup
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setup(
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name='store',
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description='A database interface to store MD evaluations.',
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author_email='niels.mueller@physik.tu-darmstadt.de',
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packages=['store', 'store.webview'],
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version='0.2',
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requires=['sqlalchemy', 'psycopg2', 'pandas'],
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zip_safe=False,
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include_package_data=True,
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package_data={'store': ['store.cfg'], 'store.webview': [
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'templates/*', 'static/bootstrap_v4/*/*', 'static/jquery_v3/*', 'static/popper_v1/*']},
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entry_points={
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'console_scripts': [
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'mdeval = store.eval:cli',
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'store-dump = store.store:dump_cli'
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]
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},
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)
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store/__init__.py
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store/__init__.py
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import os
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import configparser
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import socket
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config = configparser.ConfigParser()
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config.read([
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os.path.join(os.path.dirname(__file__), 'store.cfg'),
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os.path.expanduser('~/.store.cfg'),
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os.environ.get('STORE_CONFIG', '')
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])
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PGPASS = '/nfsopt/mdevaluate/pgpass'
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if os.path.exists(PGPASS):
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with open(PGPASS) as f:
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for pgpass in f:
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hostname, *_, username, password = pgpass.split(':')
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if hostname == 'db.cluster' and username == 'store':
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config['store']['pg_password'] = password.strip()
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# we sometimes have problems with the internal DNS, therefore try to resolve
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# the database host in advance and use IP directly
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try:
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config['store']['pg_host'] = socket.gethostbyname(config['store']['pg_host'])
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except OSError:
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pass
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from .store import get, update, delete, init_db, observables, systems, merge, dump_db
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__all__ = ['get', 'update', 'delete', 'init_db', 'observables', 'systems', 'merge', 'dump_db']
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store/analyse.py
Executable file
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store/analyse.py
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from functools import partial
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import numpy as np
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import pandas as pd
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from scipy.optimize import curve_fit
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import mdevaluate as md
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import store
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from .utils import data_frame, traj_slice, set_correlation_defaults, collect_short, excess_entropy, enhanced_bins
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def openNojump(path, maxcache=500):
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trajectory = md.open(path, trajectory='nojump.xtc', cached=maxcache)
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return trajectory
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def savetxt_newer(filename, newData):
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if not os.path.isfile(filename):
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np.savetxt(filename, newData)
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return
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f = NamedTemporaryFile()
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np.savetxt(f.name, newData)
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if not filecmp.cmp(filename, f.name):
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np.savetxt(filename, newData)
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f.close()
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return
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def isf(trajectory, q, nojump=True, nav=3, outdir=None, **kwargs):
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"""
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Compute the incoherent intermediate scattering function and and meta analyses.
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Meta analyses include variance in time, correlation time and susceptibility.
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"""
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kwargs = set_correlation_defaults(kwargs)
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kwargs['average'] = False
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description = 'isf'
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if 'description' in kwargs:
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description += '_' + kwargs.pop('description')
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if nojump:
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trajectory = trajectory.nojump
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t, S = md.correlation.shifted_correlation(
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partial(md.correlation.isf, q=q), trajectory,
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description=description, **kwargs)
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N = len(trajectory[0])
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time = md.utils.runningmean(t[1:], nav)
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χ4 = md.utils.runningmean(N * S.var(axis=0)[1:], nav)
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S = S.mean(axis=0)
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freq, suscept = md.correlation.susceptibility(t, S)
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result = {
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'isf': data_frame(time=t, cor=S),
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'isf_var': data_frame(time=time, var=χ4),
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'isf_sus': data_frame(freq=freq, sus=suscept)
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}
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try:
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m = (S < 0.7)
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tau = t[np.absolute(S - 1 / np.e).argmin()]
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fit, _ = curve_fit(md.functions.kww, t[m], S[m], p0=(1, tau, 1), maxfev=5000)
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tau_1e = md.functions.kww_1e(*fit)
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result['isf_tau'] = tau_1e
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except RuntimeError:
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md.logger.info('Could not estimate tau: %s', trajectory)
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return result
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||||
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||||
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||||
# wraps around isf, determines automatic
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||||
def isfwater(trajectory, storeparam, **kwargs):
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kwargs['segments'] = 10000000 // len(trajectory[0])
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t, S = md.correlation.shifted_correlation(partial(md.correlation.isf, q=22.7), trajectory,
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segments=min(5, kwargs['segments'] // 50), window=0.5, skip=0.1,
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average=True, description='rough')
|
||||
mask = (S < 0.9) & (S > 0.1)
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||||
with np.errstate(invalid='ignore'):
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fit, _ = curve_fit(md.functions.kww, t[mask], S[mask])
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||||
tau_est = md.functions.kww_1e(*fit)
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time = trajectory[-1].time - trajectory[0].time
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||||
kwargs['window'] = max(min(500 * tau_est / time, 0.5), 0.01)
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kwargs['skip'] = max(0.01, min(0.1, 2 * tau_est / time))
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||||
return isf(trajectory, storeparam, q=22.7, nojump=False, **kwargs)
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||||
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||||
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||||
def csf(trajectory, q, nav=3, **kwargs):
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||||
"""Compute the coherent intermediate scattering function and its variance."""
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||||
kwargs = set_correlation_defaults(kwargs)
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||||
kwargs['average'] = False
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||||
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||||
t, S = md.correlation.shifted_correlation(
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||||
partial(md.correlation.coherent_scattering_function, q=q),
|
||||
trajectory.pbc,
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||||
**kwargs
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||||
)
|
||||
|
||||
csf_variance = data_frame(
|
||||
time=md.utils.runningmean(t, nav),
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||||
χ4=md.utils.runningmean(S.var(axis=0), nav)
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||||
)
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||||
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return {'csf': data_frame(time=t, csf=S.mean(axis=0)), 'csf_variance': csf_variance}
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||||
|
||||
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||||
def msd(trajectory, **kwargs):
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||||
"""Compute the mean squared displacement."""
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||||
kwargs = set_correlation_defaults(kwargs)
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||||
kwargs.setdefault('average', True)
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||||
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||||
@collect_short
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||||
def calc(trajectory, **kwargs):
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||||
t, S = md.correlation.shifted_correlation(
|
||||
md.correlation.msd,
|
||||
trajectory.nojump,
|
||||
**kwargs
|
||||
)
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||||
return {'msd': data_frame(time=t, msd=S)}
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||||
|
||||
res = calc(trajectory, **kwargs)
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||||
|
||||
# Mean diffusivity, calculated over the last half-decade.
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||||
t = res['msd'].time.values
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||||
S = res['msd'].msd.values
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||||
m = t > (t.max() / 3.16)
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||||
D = (S[m] / (6 * t[m])).mean()
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||||
res['D'] = D
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||||
return res
|
||||
|
||||
|
||||
def tetrahedral_order(trajectory, other=None, skip=0.1, nr_averages=500, normed=True, **kwargs):
|
||||
if other is None:
|
||||
other = trajectory
|
||||
bins = np.arange(-3, 1, 0.01)
|
||||
q = md.utils.runningmean(bins, 2)
|
||||
sl = traj_slice(len(trajectory), skip, nr_averages)
|
||||
res = md.distribution.time_average(
|
||||
partial(md.distribution.tetrahedral_order_distribution, bins=bins),
|
||||
trajectory.pbc[sl],
|
||||
coordinates_b=other.pbc[sl],
|
||||
**kwargs
|
||||
)
|
||||
N = len(trajectory[0]) if normed else 1
|
||||
res /= N
|
||||
tet_mean = data_frame(**{'<Q>': sum(res * q), 'S_Q': sum(res * np.log(1 - q))})
|
||||
return {'tetrahedral_order': data_frame(q=q, distribution=res),
|
||||
'tetrahedral_mean': tet_mean}
|
||||
|
||||
|
||||
def vector(trajectory, atoms=None):
|
||||
"""
|
||||
Calcuate the vectors between two types of atoms in the trajectory.
|
||||
|
||||
The names of the atoms between which the vectors should be calculated can be either given
|
||||
as a list of length 2, or the trajectory should contain excactly two atom types.
|
||||
"""
|
||||
if atoms is None:
|
||||
atoms = sorted(list(set(trajectory.atom_subset.atom_names)))
|
||||
assert len(atoms) == 2, 'Need to specifiy excactly two atom types for vector calculation.'
|
||||
at_a, at_b = atoms
|
||||
box = trajectory[0].box.diagonal()
|
||||
atoms_a = trajectory.atom_subset.atom_names == at_a
|
||||
atoms_b = trajectory.atom_subset.atom_names == at_b
|
||||
return md.coordinates.vectors(trajectory, atoms_a=atoms_a, atoms_b=atoms_b, normed=True, box=box)
|
||||
|
||||
|
||||
def water_dipole(trajectory):
|
||||
"""Create a cordinates map of normed water dipole vectors."""
|
||||
sel = trajectory.atom_subset.selection
|
||||
atoms_a = np.where(trajectory.subset(atom_name='OW').atom_subset.selection[sel])[0]
|
||||
atoms_b = np.where(trajectory.subset(atom_name='HW.').atom_subset.selection[sel])[0]
|
||||
atoms_b = atoms_b.reshape(len(atoms_a), 2).T
|
||||
box = trajectory[0].box.diagonal()
|
||||
vec = md.coordinates.vectors(trajectory, atoms_a=atoms_a, atoms_b=atoms_b, normed=True, box=box)
|
||||
vec.description = 'water-dipole'
|
||||
return vec
|
||||
|
||||
|
||||
def water_OH_bonds(trajectory):
|
||||
"""Create a coordinates map of normed OH vectors for water molecules."""
|
||||
sel = trajectory.atom_subset.selection
|
||||
atoms_a = np.where(trajectory.subset(atom_name='OW').atom_subset.selection[sel])[0]
|
||||
atoms_b = np.where(trajectory.subset(atom_name='HW.').atom_subset.selection[sel])[0]
|
||||
atoms_a = np.vstack([atoms_a] * 2).T.reshape(atoms_b.shape)
|
||||
box = trajectory[0].box.diagonal()
|
||||
vec = md.coordinates.vectors(trajectory, atoms_a=atoms_a, atoms_b=atoms_b, normed=True, box=box)
|
||||
vec.description = 'water-OH-bonds'
|
||||
return vec
|
||||
|
||||
|
||||
def oaf(trajectory, order, nav=1, **kwargs):
|
||||
"""
|
||||
Calculate the orientational autocorrelation function and meta analyses.
|
||||
|
||||
Use in conjunction with a coordinates map, like water_dipole, to map atom coordinates to the
|
||||
desired vectors. Meta anaylsis include the functions variance in time, correlation time and
|
||||
the susceptibility. Results are called F{order} (i.e. F1, F2) and accordingly.
|
||||
|
||||
Args:
|
||||
trajectory: The correlated vectore, will be passed automatically in automatic evaluations.
|
||||
order: Order of the used legendre polynomial, typically 1 or 2.
|
||||
nav (opt.): Running average bevor calculating variance
|
||||
**kwargs: Any keyowrd arguments are passed to the time_average function.
|
||||
"""
|
||||
kwargs = set_correlation_defaults(kwargs)
|
||||
|
||||
fdesc = 'F{}'.format(order)
|
||||
description = fdesc
|
||||
if 'description' in kwargs:
|
||||
description += '_' + kwargs.pop('description')
|
||||
|
||||
# Collect short should apply to the basic compuations only,
|
||||
# additional meta analyses, like tau and susceptibility, are computed from the result.
|
||||
@collect_short
|
||||
def calc_oaf(vectors, order, nav=1, **kwargs):
|
||||
kwargs['average'] = False
|
||||
t, F = md.correlation.shifted_correlation(
|
||||
partial(md.correlation.rotational_autocorrelation, order=order),
|
||||
vectors,
|
||||
description=description,
|
||||
**kwargs
|
||||
)
|
||||
result = {fdesc: data_frame(time=t, cor=F.mean(axis=0))}
|
||||
Na = len(vectors[0])
|
||||
result[fdesc + '_var'] = data_frame(
|
||||
time=md.utils.runningmean(t, nav), var=md.utils.runningmean(Na * F.var(axis=0), nav)
|
||||
)
|
||||
return result
|
||||
|
||||
res = calc_oaf(trajectory, order, nav=nav, **kwargs)
|
||||
t, F = res[fdesc].time.values, res[fdesc].cor.values
|
||||
if F.min() < 0.3:
|
||||
res[fdesc + '_tau'] = md.utils.quick1etau(t, F)
|
||||
freq, sus = md.correlation.susceptibility(t, F)
|
||||
res[fdesc + '_sus'] = data_frame(freq=freq, sus=sus)
|
||||
return res
|
||||
|
||||
|
||||
def rdf(trajectory, other=None, skip=0.01, nr_averages=100, q=None, kind=None, **kwargs):
|
||||
"""
|
||||
Compute radial pair-distribution function, static structure factor and pair entropy.
|
||||
|
||||
The quantities can be calculated for one ore two sets of atoms. The bins of g(r) are
|
||||
determined automatically, with rmax = L/2 and variable bins with a maximal width of 0.01.
|
||||
|
||||
Args:
|
||||
trajectory: First set of atoms
|
||||
other (opt.): Second set of atoms.
|
||||
skip (opt.): Part of the trajectory to skip at the beginning
|
||||
nr_averages (opt.): How many averages should be taken
|
||||
q (opt.): Scattering vectors of S(q). Default is 2π/(L/2) < q <2π/0.1, with Δq=0.2.
|
||||
"""
|
||||
bins = np.arange(0.0, trajectory[0].box.diagonal().min() / 2, 0.001)
|
||||
r = md.utils.runningmean(bins, 2)
|
||||
sl = traj_slice(len(trajectory), skip, nr_averages)
|
||||
if other is not None:
|
||||
kwargs['coordinates_b'] = other.pbc[sl]
|
||||
|
||||
res = md.distribution.time_average(
|
||||
partial(md.distribution.rdf, bins=bins, kind=kind),
|
||||
trajectory.pbc[sl],
|
||||
**kwargs
|
||||
)
|
||||
|
||||
L = trajectory[0].box.diagonal().min()
|
||||
if q is None:
|
||||
q = 2 * np.pi * np.arange(1 / L, 10, 0.5 / L)
|
||||
Nb = len(other[0]) if other is not None else len(trajectory[0])
|
||||
ρ = Nb / trajectory[0].volume
|
||||
Sq = md.utils.Sq_from_gr(r, res, q, ρ)
|
||||
|
||||
ρ = len(trajectory[0]) / trajectory[0].volume
|
||||
S_excess = excess_entropy(r, res, ρ)
|
||||
|
||||
return {'rdf': data_frame(r=r, rdf=res), 'structure_factor': data_frame(q=q, Sq=Sq),
|
||||
'excess_entropy': S_excess}
|
403
store/eval.py
Executable file
403
store/eval.py
Executable file
@ -0,0 +1,403 @@
|
||||
import os
|
||||
import filecmp
|
||||
import re
|
||||
from tempfile import NamedTemporaryFile
|
||||
import argparse
|
||||
from psutil import virtual_memory, cpu_count
|
||||
import inspect
|
||||
import yaml
|
||||
from glob import glob
|
||||
from multiprocessing.pool import Pool
|
||||
import traceback
|
||||
from datetime import datetime, timedelta
|
||||
import functools
|
||||
from enum import Enum
|
||||
import time
|
||||
from pathlib import Path
|
||||
|
||||
from sqlalchemy.exc import OperationalError
|
||||
|
||||
import pydoc
|
||||
|
||||
import numpy as np
|
||||
|
||||
import mdevaluate as md
|
||||
from mdevaluate.logging import logger
|
||||
|
||||
from . import store
|
||||
from . import config
|
||||
|
||||
|
||||
def locate(fname, namespace=''):
|
||||
return pydoc.locate(namespace + '.' + fname) or pydoc.locate('store.analyse.' + fname)
|
||||
|
||||
|
||||
def open_sim(directory, maxcache=None):
|
||||
tr = None
|
||||
if len(glob(os.path.join(directory, 'nojump.xtc'))) is 1:
|
||||
tr = md.open(directory, trajectory='nojump.xtc', cached=maxcache, reindex=True)
|
||||
else:
|
||||
tr = md.open(directory, trajectory='out/*.xtc', cached=maxcache, reindex=True, nojump=True)
|
||||
if tr is None:
|
||||
raise FileNotFoundError('Can not open trajectory.')
|
||||
return tr
|
||||
|
||||
|
||||
def open_energy(directory):
|
||||
return md.open_energy(os.path.join(directory, 'out/*.edr'))
|
||||
|
||||
|
||||
def dataframe_to_txt(fname, df):
|
||||
"""Save a dataframe to textfile."""
|
||||
header = ' '.join(df.columns)
|
||||
np.savetxt(fname, df.values, header=header)
|
||||
|
||||
|
||||
class RunState:
|
||||
OK = 0
|
||||
ERROR = 1
|
||||
UNKNOWN = 2
|
||||
|
||||
def __init__(self, st, timing=None):
|
||||
if isinstance(st, str):
|
||||
self.state = getattr(self, st)
|
||||
else:
|
||||
self.state = st
|
||||
self.timing = timing
|
||||
|
||||
def __str__(self):
|
||||
if self.state == self.OK:
|
||||
s = '\x1b[0;32m\u2713\x1b[0m'
|
||||
if self.timing is not None:
|
||||
s += '({})'.format(self.timing)
|
||||
return s
|
||||
elif self.state == self.ERROR:
|
||||
return '\x1b[0;31m\u2717\x1b[0m'
|
||||
elif self.state == self.UNKNOWN:
|
||||
return '\x1b[0;33m?\x1b[0m'
|
||||
|
||||
|
||||
@functools.total_ordering
|
||||
class Report:
|
||||
|
||||
def apply(self, func, *args, err_count=1, **kwargs):
|
||||
if isinstance(func, functools.partial):
|
||||
fname = func.func.__name__
|
||||
else:
|
||||
fname = func.__name__
|
||||
try:
|
||||
start = datetime.now()
|
||||
res = func(*args, **kwargs)
|
||||
time = timedelta(seconds=round((datetime.now() - start).total_seconds()))
|
||||
self.runok(fname, timing=time)
|
||||
return res
|
||||
except Exception as e:
|
||||
self.runerror(fname)
|
||||
self.error(e, err_count=err_count)
|
||||
|
||||
def runok(self, name, timing=None):
|
||||
# st = RunStates.OK.timing(timing) if timing is not None else RunStates.OK
|
||||
self.current['runs'].append((name, RunState('OK', timing)))
|
||||
|
||||
def runerror(self, name):
|
||||
self.current['runs'].append((name, RunState('ERROR')))
|
||||
|
||||
def unknown(self, name):
|
||||
self.current['runs'].append((name, RunState('UNKNOWN')))
|
||||
|
||||
def error(self, e, err_count=1):
|
||||
if err_count > 0:
|
||||
traceback.print_exc()
|
||||
self.current['errors'].append(e)
|
||||
self.err_count += err_count
|
||||
|
||||
def system(self, sys):
|
||||
self.systems.setdefault(sys, {'runs': [], 'errors': []})
|
||||
self.current_system = sys
|
||||
|
||||
def __repr__(self):
|
||||
rep = ''
|
||||
for sys in self.systems:
|
||||
rep += '--= {} =--\n'.format(sys)
|
||||
for run, state in self.systems[sys]['runs']:
|
||||
rep += '{}:{} '.format(run, state)
|
||||
rep += '\n'
|
||||
for e in self.systems[sys]['errors']:
|
||||
rep += str(e) + '\n'
|
||||
rep += '\n'
|
||||
return rep
|
||||
|
||||
@property
|
||||
def current(self):
|
||||
return self.systems[self.current_system]
|
||||
|
||||
@property
|
||||
def nerrors(self):
|
||||
return sum(len(sys['errors']) for sys in self.systems.values())
|
||||
|
||||
def __init__(self):
|
||||
self.systems = {}
|
||||
self.current_system = None
|
||||
self.err_count = 0
|
||||
|
||||
def __eq__(self, other):
|
||||
return self.systems == other.systems
|
||||
|
||||
def __lt__(self, other):
|
||||
return self.err_count < other.err_count
|
||||
|
||||
|
||||
class Loader(yaml.Loader):
|
||||
|
||||
def include(self, node):
|
||||
fname = os.path.abspath(self.construct_scalar(node))
|
||||
with open(fname, 'r') as f:
|
||||
return yaml.load(f, Loader)
|
||||
|
||||
def calc(self, node):
|
||||
return eval(self.construct_scalar(node))
|
||||
|
||||
|
||||
Loader.add_constructor('!include', Loader.include)
|
||||
Loader.add_constructor('!calc', Loader.calc)
|
||||
|
||||
|
||||
def find_user():
|
||||
return os.environ.get('USER') or os.environ.get('LOGNAME')
|
||||
|
||||
|
||||
def run_eval(yamlfile, debug=False, txtout=None, autosavedir=None):
|
||||
"""
|
||||
Read an eval.yaml file and run the specified functions and store the result.
|
||||
"""
|
||||
report = Report()
|
||||
with open(yamlfile) as f:
|
||||
yaml_dict = yaml.load(f.read(), Loader)
|
||||
|
||||
directory = os.path.dirname(yamlfile)
|
||||
user = find_user()
|
||||
namespace = yaml_dict.pop('namespace', '')
|
||||
report.system(directory)
|
||||
|
||||
for k, v in yaml_dict.pop('config', {}).items():
|
||||
config['eval'][k] = str(v)
|
||||
|
||||
temperature = yaml_dict['simulation_params'].pop('T', None)
|
||||
if temperature is None:
|
||||
m = re.match('.*[^\d](\d+)K.*', directory)
|
||||
if m is not None:
|
||||
temperature = int(m.group(1))
|
||||
|
||||
if debug:
|
||||
print('Evaluation for', directory)
|
||||
print('User:', user)
|
||||
print('T:', temperature)
|
||||
|
||||
# dont overdo caching, this allows several parallel analysis with caching
|
||||
MAXCACHE = int(min(3000, (virtual_memory().total / 1024**2 / 5 / cpu_count() / 0.4) // 10 * 10))
|
||||
if autosavedir is not None:
|
||||
md.autosave.enable(autosavedir, verbose=True)
|
||||
|
||||
if 'trajectory-open' in yaml_dict:
|
||||
fopen = locate(yaml_dict['trajectory-open'], namespace)
|
||||
if fopen is None:
|
||||
raise ValueError("Trajectory loader couldn't be located: {}".format(yaml_dict['trajectory-open']))
|
||||
else:
|
||||
fopen = open_sim
|
||||
traj = report.apply(fopen, directory, maxcache=config['eval'].getint('maxcache', MAXCACHE))
|
||||
|
||||
if 'energy-open' in yaml_dict:
|
||||
eopen = locate(yaml_dict['energy-open'], namespace)
|
||||
eopen_err_count = 1
|
||||
if fopen is None:
|
||||
raise ValueError("Energy loader couldn't be located: {}".format(yaml_dict['energy-open']))
|
||||
else:
|
||||
eopen = open_energy
|
||||
eopen_err_count = 0
|
||||
energyfile = report.apply(eopen, directory, err_count=eopen_err_count)
|
||||
|
||||
if config.getboolean('eval', 'require_trajectory') and traj is None:
|
||||
return report
|
||||
if traj is None and energyfile is None:
|
||||
return report
|
||||
|
||||
logger.info('Running evaluations for: %s', directory)
|
||||
for evaluation in yaml_dict['evaluations']:
|
||||
subset = evaluation['subset']
|
||||
selection = subset.pop('selection')
|
||||
|
||||
if 'coordinates-map' in subset:
|
||||
cmap = subset.pop('coordinates-map')
|
||||
crds_map = locate(cmap, namespace)
|
||||
if crds_map is None:
|
||||
report.unknown(cmap)
|
||||
continue
|
||||
subtraj = crds_map(traj.subset(**subset)) if traj is not None else None
|
||||
else:
|
||||
subtraj = traj.subset(**subset) if traj is not None else None
|
||||
subtraj.selection = selection
|
||||
|
||||
other = evaluation.pop('other', None)
|
||||
if other is not None and traj is not None:
|
||||
selection += '-' + other.pop('selection')
|
||||
if 'coordinates-map' in other:
|
||||
cmap = other.pop('coordinates-map')
|
||||
crds_map = locate(cmap, namespace)
|
||||
if crds_map is None:
|
||||
report.unknown(cmap)
|
||||
continue
|
||||
othertraj = crds_map(traj.subset(**other))
|
||||
else:
|
||||
othertraj = traj.subset(**other)
|
||||
else:
|
||||
othertraj = None
|
||||
|
||||
functions = evaluation.pop('functions')
|
||||
|
||||
report.system('{}@{}'.format(selection, directory))
|
||||
if debug:
|
||||
print('*****')
|
||||
print('subset:', subset)
|
||||
print('selection:', selection)
|
||||
print('subtraj:', subtraj)
|
||||
for func in functions:
|
||||
if isinstance(func, dict):
|
||||
if len(func) == 1:
|
||||
(func, params), = func.items()
|
||||
else:
|
||||
logger.info('Function definition is unclear: %s', str(func))
|
||||
else:
|
||||
params = {}
|
||||
if othertraj is not None:
|
||||
params['other'] = othertraj
|
||||
# Locate the function: First under a specified namespace, then in the default module
|
||||
f = locate(namespace + '.' + func) or locate('store.analyse.' + func)
|
||||
if f is not None:
|
||||
if debug:
|
||||
print('---')
|
||||
print('function:', f, func)
|
||||
print('params:', params)
|
||||
report.runok(func)
|
||||
else:
|
||||
logger.info('Run function %s', func)
|
||||
func_args = inspect.signature(f).parameters
|
||||
if 'trajectory' in func_args:
|
||||
params['trajectory'] = subtraj
|
||||
if 'energyfile' in func_args:
|
||||
params['energyfile'] = energyfile
|
||||
res = report.apply(f, **params)
|
||||
if not isinstance(res, dict):
|
||||
res = {func: res}
|
||||
params.pop('trajectory', None)
|
||||
params.pop('other', None)
|
||||
params.pop('energyfile', None)
|
||||
for obs, data in res.items():
|
||||
if txtout is not None:
|
||||
dataframe_to_txt(os.path.join(txtout, '{}.dat'.format(obs)), data)
|
||||
store.update(
|
||||
obs, data, directory=directory, user=user, selection=selection, T=temperature,
|
||||
simulation_params=yaml_dict.get('simulation_params', {}),
|
||||
evaluation_params=params
|
||||
)
|
||||
else:
|
||||
report.unknown(func)
|
||||
logger.info('Function %s was not found. Namespace was: %s', func, namespace)
|
||||
|
||||
return report
|
||||
|
||||
|
||||
def recursive_analysis(basedir, processes=None, debug=False, txtout=None, autosavedir=None):
|
||||
"""
|
||||
Run analysis functions recursively for baseidr on several processes.
|
||||
"""
|
||||
logger.info('Starting recursive analysis in directory: {}'.format(basedir))
|
||||
reports = []
|
||||
|
||||
def collect_reports(rep):
|
||||
reports.append(rep)
|
||||
|
||||
def catch_error(err):
|
||||
traceback.print_exception(type(err), err, err.__traceback__)
|
||||
|
||||
yaml_files = [str(y) for p in glob(basedir) for y in Path(p).glob('**/eval.yaml')]
|
||||
|
||||
logger.info('Finished walking directories:')
|
||||
for y in yaml_files:
|
||||
logger.info(y)
|
||||
|
||||
# Evaluation is syncronous only if processes=False.
|
||||
if processes is False:
|
||||
for y in yaml_files:
|
||||
print(y)
|
||||
try:
|
||||
reports.append(run_eval(y, debug=debug, txtout=txtout, autosavedir=autosavedir))
|
||||
except FileNotFoundError:
|
||||
print('Skipping evaluation...')
|
||||
else:
|
||||
#pool = Pool(processes=processes)
|
||||
#for y in yaml_files:
|
||||
# pool.apply_async(run_eval, args=(y,), kwds={'debug': debug, 'txtout': txtout, 'autosavedir': autosavedir},
|
||||
# callback=collect_reports, error_callback=catch_error)
|
||||
#pool.close()
|
||||
#pool.join()
|
||||
with Pool(processes=processes) as pool:
|
||||
for y in yaml_files:
|
||||
time.sleep(5)
|
||||
pool.apply_async(run_eval, args=(y,), kwds={'debug': debug, 'txtout': txtout, 'autosavedir': autosavedir},
|
||||
callback=collect_reports, error_callback=catch_error)
|
||||
pool.close()
|
||||
pool.join()
|
||||
# reports = pool.map(
|
||||
# functools.partial(run_eval, debug=debug, txtout=txtout, autosavedir=autosavedir),
|
||||
# yaml_files
|
||||
# )
|
||||
|
||||
print('#*' * 22)
|
||||
print('Finished analysis!: {}'.format(datetime.strftime(datetime.now(), '%c')))
|
||||
print('#*' * 22)
|
||||
for rep in sorted(reports):
|
||||
print(rep)
|
||||
if len(yaml_files) != len(reports):
|
||||
print('#### Error: {} / {} tasks were reported.'.format(len(reports), len(yaml_files)))
|
||||
for y in yaml_files:
|
||||
root = os.path.dirname(y)
|
||||
if not any(root in str(rep) for rep in reports):
|
||||
print('Task not reported: {}'.format(root))
|
||||
|
||||
|
||||
# ===========================================
|
||||
def cli(args=None):
|
||||
parser = argparse.ArgumentParser(description='Analyse a certain simulation')
|
||||
parser.add_argument('--recursive', '-r', action='store_true', default=False,
|
||||
help='Perform a recusrive evaluation of the directory.')
|
||||
parser.add_argument('-d', default=None, help='simulation directory; default cwd')
|
||||
parser.add_argument('-o', default=None,
|
||||
help='default None; output directory for human readable *.dat, if this is not a path ending with "/" then the last part will be a common prefix')
|
||||
parser.add_argument('--autosave', '-a', default=None, help='Autosave directory')
|
||||
parser.add_argument('--verbose', '-v', default=False, action='store_true',
|
||||
help='Be verbose, i.e. set logging level to DEBUG, default is INFO')
|
||||
parser.add_argument('--processes', '-np', default=None, type=int,
|
||||
help='Number of sub-processes for the recursive evaluation.')
|
||||
args = parser.parse_args()
|
||||
if args.verbose:
|
||||
md.logging.setlevel('DEBUG')
|
||||
SIMDIR = args.d
|
||||
if SIMDIR is None:
|
||||
SIMDIR = os.getcwd()
|
||||
SIMDIR = os.path.abspath(SIMDIR)
|
||||
OUTDIR = args.o
|
||||
if OUTDIR is not None:
|
||||
OUTDIR = os.path.abspath(OUTDIR)
|
||||
if args.o[-1] == '/':
|
||||
OUTDIR = OUTDIR + '/'
|
||||
|
||||
if args.recursive:
|
||||
recursive_analysis(SIMDIR, txtout=OUTDIR, autosavedir=args.autosave, processes=args.processes)
|
||||
else:
|
||||
yamlfile = os.path.join(SIMDIR, 'eval.yaml')
|
||||
if os.path.exists(yamlfile):
|
||||
rep = run_eval(yamlfile, txtout=OUTDIR, autosavedir=args.autosave)
|
||||
print(rep)
|
||||
else:
|
||||
print('eval.yaml not found, exiting')
|
||||
quit()
|
24
store/store.cfg
Normal file
24
store/store.cfg
Normal file
@ -0,0 +1,24 @@
|
||||
[store]
|
||||
# The database connection - change this to sqlite://store.db to use a local sqlite database
|
||||
pg_host = db.cluster
|
||||
pg_port = 5432
|
||||
pg_user = store
|
||||
pg_password = none
|
||||
db_file = postgresql://%(pg_user)s:%(pg_password)s@%(pg_host)s:%(pg_port)s/store
|
||||
|
||||
[eval]
|
||||
|
||||
require_trajectory = True
|
||||
maxcache = 2000
|
||||
|
||||
topology = *.tpr
|
||||
trajectory = out/*.xtc
|
||||
short_dir = ../short/*
|
||||
|
||||
nojump = True
|
||||
|
||||
[correlation]
|
||||
|
||||
skip = 0.01
|
||||
window = 0.3
|
||||
segments = 300
|
500
store/store.py
Executable file
500
store/store.py
Executable file
@ -0,0 +1,500 @@
|
||||
import os
|
||||
from collections.abc import Iterable
|
||||
from logging import info
|
||||
import argparse
|
||||
import pickle
|
||||
|
||||
import pandas as pd
|
||||
import sqlalchemy as sql
|
||||
from sqlalchemy.ext.declarative import declarative_base
|
||||
from sqlalchemy.pool import NullPool
|
||||
|
||||
|
||||
from .utils import numlike, number_shorthand, lazy_eq
|
||||
from . import config
|
||||
|
||||
|
||||
Base = declarative_base()
|
||||
Engine = sql.create_engine(config['store']['db_file'], poolclass=NullPool)
|
||||
Session = sql.orm.sessionmaker(bind=Engine)
|
||||
|
||||
|
||||
def init_db():
|
||||
pass
|
||||
|
||||
|
||||
class FloatAttribute(Base):
|
||||
__tablename__ = 'floatattributes'
|
||||
id = sql.Column(sql.Integer, primary_key=True)
|
||||
name = sql.Column(sql.String)
|
||||
value = sql.Column(sql.Float)
|
||||
simulation_id = sql.Column(sql.Integer, sql.ForeignKey('simulations.id'))
|
||||
|
||||
def __init__(self, name, value):
|
||||
self.name = name
|
||||
self.value = value
|
||||
|
||||
def __repr__(self):
|
||||
return '<{classname}({name}={value})>'.format(
|
||||
classname=self.__class__.__name__, name=self.name, value=self.value
|
||||
)
|
||||
|
||||
|
||||
class StringAttribute(Base):
|
||||
__tablename__ = 'stringattributes'
|
||||
id = sql.Column(sql.Integer, primary_key=True)
|
||||
name = sql.Column(sql.String)
|
||||
value = sql.Column(sql.String)
|
||||
simulation_id = sql.Column(sql.Integer, sql.ForeignKey('simulations.id'))
|
||||
|
||||
def __init__(self, name, value):
|
||||
self.name = name
|
||||
self.value = value
|
||||
|
||||
def __repr__(self):
|
||||
return '<{classname}({name}={value})>'.format(
|
||||
classname=self.__class__.__name__, name=self.name, value=self.value
|
||||
)
|
||||
|
||||
|
||||
class Parameter(Base):
|
||||
__tablename__ = 'parameters'
|
||||
id = sql.Column(sql.Integer, primary_key=True)
|
||||
name = sql.Column(sql.String)
|
||||
value = sql.Column(sql.Float)
|
||||
evaluation_id = sql.Column(sql.Integer, sql.ForeignKey('evaluations.id'))
|
||||
|
||||
def __init__(self, name, value):
|
||||
self.name = name
|
||||
self.value = value
|
||||
|
||||
def __repr__(self):
|
||||
return '<{classname}({name}={value})>'.format(
|
||||
classname=self.__class__.__name__, name=self.name, value=self.value
|
||||
)
|
||||
|
||||
|
||||
class Simulation(Base):
|
||||
__tablename__ = 'simulations'
|
||||
|
||||
id = sql.Column(sql.Integer, primary_key=True)
|
||||
directory = sql.Column(sql.String)
|
||||
user = sql.Column(sql.String)
|
||||
temperature = sql.Column(sql.Float)
|
||||
|
||||
float_params = sql.orm.relationship(FloatAttribute)
|
||||
string_params = sql.orm.relationship(StringAttribute)
|
||||
|
||||
evaluations = sql.orm.relationship('Evaluation', order_by='Evaluation.id', back_populates='simulation')
|
||||
|
||||
def add_attribute(self, name, value):
|
||||
self.attributes.append(FloatAttribute(name, value))
|
||||
|
||||
def add_parameter(self, name, value):
|
||||
if numlike(value):
|
||||
self.float_params.append(FloatAttribute(name, value))
|
||||
else:
|
||||
self.string_params.append(StringAttribute(name, value))
|
||||
|
||||
def copy(self):
|
||||
params = {p.name: p.value for p in self.float_params + self.string_params}
|
||||
|
||||
return Simulation(self.directory, self.user, self.temperature, **params)
|
||||
|
||||
def delete(self, session=None):
|
||||
if session is None:
|
||||
session = Session()
|
||||
|
||||
for e in self.evaluations:
|
||||
e.delete(session=session)
|
||||
|
||||
for p in self.float_params + self.string_params:
|
||||
session.delete(p)
|
||||
|
||||
session.delete(self)
|
||||
|
||||
def __init__(self, directory, user, temperature, **parameters):
|
||||
self.directory = directory or ''
|
||||
self.user = user or ''
|
||||
self.temperature = temperature
|
||||
for name, value in parameters.items():
|
||||
self.add_parameter(name, value)
|
||||
|
||||
def __repr__(self):
|
||||
attrs = []
|
||||
for attr, val in self.__dict__.items():
|
||||
if attr[0] is not '_' and attr is not 'type':
|
||||
attrs.append('{}={}'.format(attr, val))
|
||||
return '<{classname}({attributes})>'.format(classname=self.__class__.__name__, attributes=', '.join(attrs))
|
||||
|
||||
|
||||
# Dataframes can only be unpickled with the same version of Pandas used to store them
|
||||
class PandasPickler:
|
||||
|
||||
@staticmethod
|
||||
def dumps(obj, protocol=None):
|
||||
if isinstance(obj, pd.DataFrame):
|
||||
obj = obj.to_dict()
|
||||
return pickle.dumps(obj, protocol=protocol)
|
||||
|
||||
@staticmethod
|
||||
def loads(buf):
|
||||
obj = pickle.loads(buf)
|
||||
if isinstance(obj, dict):
|
||||
obj = pd.DataFrame(obj)
|
||||
return obj
|
||||
|
||||
|
||||
class Evaluation(Base):
|
||||
__tablename__ = 'evaluations'
|
||||
|
||||
id = sql.Column(sql.Integer, primary_key=True)
|
||||
simulation_id = sql.Column(sql.Integer, sql.ForeignKey('simulations.id'))
|
||||
observable = sql.Column(sql.String)
|
||||
selection = sql.Column(sql.String)
|
||||
data = sql.Column(sql.PickleType(comparator=lazy_eq, pickler=PandasPickler))
|
||||
parameters = sql.orm.relationship('Parameter')
|
||||
|
||||
simulation = sql.orm.relationship('Simulation', back_populates='evaluations')
|
||||
|
||||
@property
|
||||
def dataframe(self):
|
||||
"""
|
||||
Return a dataframe representing the evaluated data and meta data of the evaluation.
|
||||
"""
|
||||
if self.data is None:
|
||||
df = pd.DataFrame()
|
||||
elif numlike(self.data):
|
||||
df = pd.DataFrame({self.observable: self.data}, index=[0])
|
||||
else:
|
||||
df = self.data.copy()
|
||||
|
||||
df['selection'] = self.selection
|
||||
for p in self.parameters:
|
||||
df[p.name] = p.value
|
||||
df['directory'] = self.simulation.directory
|
||||
df['user'] = self.simulation.user
|
||||
df['T'] = self.simulation.temperature
|
||||
for a in self.simulation.float_params:
|
||||
df[a.name] = a.value
|
||||
for a in self.simulation.string_params:
|
||||
df[a.name] = a.value
|
||||
|
||||
return df
|
||||
|
||||
def add_parameter(self, name, value):
|
||||
self.parameters.append(Parameter(name, value))
|
||||
|
||||
def copy(self, simulation=None):
|
||||
return Evaluation(self.observable, simulation or self.simulation, self.data,
|
||||
parameters={p.name: p.value for p in self.parameters})
|
||||
|
||||
def delete(self, session=None):
|
||||
if session is None:
|
||||
session = Session()
|
||||
|
||||
for p in self.parameters:
|
||||
session.delete(p)
|
||||
session.delete(self)
|
||||
|
||||
def __init__(self, observable, simulation, data, selection='', parameters={}):
|
||||
self.observable = observable
|
||||
self.simulation = simulation
|
||||
self.data = data
|
||||
self.selection = selection
|
||||
for name, value in parameters.items():
|
||||
self.add_parameter(name, value)
|
||||
|
||||
def __repr__(self):
|
||||
attrs = []
|
||||
for attr, val in self.__dict__.items():
|
||||
if attr[0] is not '_' and attr not in ['type', 'data']:
|
||||
attrs.append('{}={}'.format(attr, val))
|
||||
return '<{classname}({attributes})>'.format(classname=self.__class__.__name__, attributes=', '.join(attrs))
|
||||
|
||||
|
||||
Base.metadata.create_all(Engine)
|
||||
|
||||
|
||||
def list_query(args, comparator):
|
||||
if isinstance(args, str):
|
||||
args = [args]
|
||||
return sql.or_(*[comparator(a) for a in args])
|
||||
|
||||
|
||||
def float_query(value, dbattr):
|
||||
if numlike(value):
|
||||
crit = dbattr == float(value)
|
||||
elif isinstance(value, str):
|
||||
limits = value.split('-')
|
||||
if len(limits) is 2:
|
||||
try:
|
||||
limits = [float(x) for x in limits]
|
||||
except:
|
||||
raise ValueError('Could not parse value={}'.format(value))
|
||||
crit = sql.and_(float(limits[0]) <= dbattr, dbattr <= float(limits[1]))
|
||||
else:
|
||||
raise ValueError('Could not parse value={}'.format(value))
|
||||
elif isinstance(value, Iterable):
|
||||
crit = dbattr.in_(value)
|
||||
else:
|
||||
raise ValueError('Could not parse {} as float value.'.format(value))
|
||||
return crit
|
||||
|
||||
|
||||
def query_simulation(directory=None, user=None, T=None, session=None, **attributes):
|
||||
if session is None:
|
||||
session = Session()
|
||||
|
||||
query = session.query(Simulation)
|
||||
if directory is not None:
|
||||
query = query.filter(list_query(directory, Simulation.directory.like))
|
||||
if user is not None:
|
||||
query = query.filter(list_query(user, Simulation.user.like))
|
||||
if T is not None:
|
||||
query = query.filter(float_query(T, Simulation.temperature))
|
||||
|
||||
for name, value in attributes.items():
|
||||
if number_shorthand(value):
|
||||
alias = sql.orm.aliased(FloatAttribute)
|
||||
query = query.join(alias).filter(sql.and_(alias.name == name, float_query(value, alias.value)))
|
||||
else:
|
||||
alias = sql.orm.aliased(StringAttribute)
|
||||
query = query.join(alias).filter(sql.and_(alias.name == name, list_query(value, alias.value.like)))
|
||||
return query
|
||||
|
||||
|
||||
def query_evaluation(observable, simulation, selection=None, session=None, **parameters):
|
||||
"""
|
||||
Query the database for evaluations.
|
||||
|
||||
Args:
|
||||
observable: Observable of the evaluation
|
||||
directory: Simulation directory as a string, or a list of the former.
|
||||
user: Username os list of users
|
||||
T: Temperature to query, can be a number, a list of numbers or a string giving a range
|
||||
selection: Selection of the simulation
|
||||
**attributes: Any attributes of the simulations as keyword arguments
|
||||
|
||||
This query function allows some shorthands for the definition of query values.
|
||||
For string comparisons the SQL statement LIKE is used, which allows the use of the wildcard '%'.
|
||||
Besides a concrete value, all arguments allow specification of a list of arguments,
|
||||
which will query any of the given values.
|
||||
Number values (i.e. temperature or any simulation attribute) can also be given as strings
|
||||
which represent a range, i. e. '100 - 150'.
|
||||
|
||||
Example:
|
||||
query_observable('isf', ['%/sys1', 'sys2'], T='100-200')
|
||||
|
||||
"""
|
||||
if session is None:
|
||||
session = Session()
|
||||
|
||||
if not isinstance(simulation, Iterable):
|
||||
simulation = [simulation]
|
||||
query = session.query(Evaluation).filter(
|
||||
Evaluation.simulation_id.in_([s.id for s in simulation]),
|
||||
Evaluation.observable == observable
|
||||
)
|
||||
if selection is not None:
|
||||
query = query.filter(list_query(selection, Evaluation.selection.like))
|
||||
for name, value in parameters.items():
|
||||
alias = sql.orm.aliased(Parameter)
|
||||
query = query.join(alias).filter(sql.and_(alias.name == name, float_query(value, alias.value)))
|
||||
|
||||
return query
|
||||
|
||||
|
||||
def get(observable, directory=None, user=None, T=None, selection=None,
|
||||
evaluation_params={}, simulation_params={}):
|
||||
"""
|
||||
Get evaluation data from the database.
|
||||
|
||||
Args:
|
||||
observable: The observable of the evaluation
|
||||
data: The data of the evaluation
|
||||
simulation: The evaluated simulation
|
||||
directory: The simulation directory
|
||||
user: User of the simulation
|
||||
T: Temperature of the simulation
|
||||
selection: Selection of the evaluation
|
||||
evaluation_params: A dict of parameters of the evaluation
|
||||
simualtion_params: A dict of parameters of the evaluation
|
||||
"""
|
||||
session = Session()
|
||||
|
||||
sim_query = query_simulation(directory, user=user, T=T, session=session, **simulation_params)
|
||||
if sim_query.count() == 0:
|
||||
return None
|
||||
#else:
|
||||
# simulations = sim_query.all()
|
||||
|
||||
if isinstance(observable, str):
|
||||
observable = [observable]
|
||||
results = []
|
||||
for obs in observable:
|
||||
evals = query_evaluation(obs, sim_query, selection=selection, session=session, **evaluation_params)
|
||||
results.extend([ev.dataframe for ev in evals])
|
||||
if len(results) > 0:
|
||||
df = pd.concat(results, ignore_index=True)
|
||||
res = df.sort_values(by=['directory', 'selection', 'T'])
|
||||
else:
|
||||
res = None
|
||||
session.close()
|
||||
return res
|
||||
|
||||
|
||||
def merge(observables, *args, **kwargs):
|
||||
"""
|
||||
Get the merged datasets of several observables.
|
||||
|
||||
Args:
|
||||
observables: List of observables
|
||||
*args, **kwargs: Additional Argmunets, passed to :func:`get`
|
||||
"""
|
||||
if len(observables) > 1:
|
||||
df = pd.merge(get(observables[0], *args, **kwargs), merge(observables[1:], *args, **kwargs))
|
||||
return df.sort_values(by=['system', 'selection', 'T'])
|
||||
else:
|
||||
return get(observables[0], *args, **kwargs)
|
||||
|
||||
|
||||
def update(observable, data, simulation=None, directory=None, user=None, T=None, selection=None,
|
||||
evaluation_params={}, simulation_params={}):
|
||||
"""
|
||||
Update an existing evaluation record or insert a new one into the database.
|
||||
|
||||
Args:
|
||||
observable: The observable of the evaluation
|
||||
data: The data of the evaluation
|
||||
simulation: The evaluated simulation
|
||||
directory: The simulation directory
|
||||
user: User of the simulation
|
||||
T: Temperature of the simulation
|
||||
selection: Selection of the evaluation
|
||||
evaluation_params: A dict of parameters of the evaluation
|
||||
simualtion_params: A dict of parameters of the evaluation
|
||||
|
||||
"""
|
||||
session = Session()
|
||||
|
||||
if simulation is None:
|
||||
sim_query = query_simulation(directory, user=user, T=T, session=session, **simulation_params)
|
||||
qu_count = sim_query.count()
|
||||
if qu_count == 0:
|
||||
simulation = Simulation(directory, user, T, **simulation_params)
|
||||
elif qu_count == 1:
|
||||
simulation = sim_query.first()
|
||||
else:
|
||||
session.close()
|
||||
raise ValueError('Found multiple simulation records while updating: {}'.format(sim_query.all()))
|
||||
|
||||
eval_query = query_evaluation(observable, simulation, selection=selection, session=session, **evaluation_params)
|
||||
qu_count = eval_query.count()
|
||||
if qu_count == 0:
|
||||
session.add(Evaluation(observable, simulation, data, selection=selection, parameters=evaluation_params))
|
||||
elif qu_count == 1:
|
||||
eval_query.first().data = data
|
||||
else:
|
||||
session.close()
|
||||
raise ValueError('Found more than one record in database while updating.')
|
||||
session.commit()
|
||||
session.close()
|
||||
|
||||
|
||||
def delete(*args, **kwargs):
|
||||
"""
|
||||
Delete evaluations from the database.
|
||||
"""
|
||||
session = Session()
|
||||
|
||||
query = query_evaluation(*args, **kwargs)
|
||||
for item in query:
|
||||
session.delete(item)
|
||||
# item.delete()
|
||||
|
||||
session.commit()
|
||||
session.close()
|
||||
|
||||
|
||||
def observables(directory=None, user=None, T=None, **parameters):
|
||||
"""
|
||||
List all observables, if system is not None for this specific system.
|
||||
"""
|
||||
query = query_simulation(directory, user=user, T=T, **parameters)
|
||||
|
||||
obs = set()
|
||||
for sim in query:
|
||||
obs.update({ev.observable for ev in sim.evaluations})
|
||||
return obs
|
||||
|
||||
|
||||
def systems(observable=None, user=None):
|
||||
"""
|
||||
List all system, if observable is not None for this specific observable.
|
||||
"""
|
||||
query = query_simulation(user=user)
|
||||
|
||||
if observable is not None:
|
||||
query = query.join(Evaluation).filter(Evaluation.observable == observable)
|
||||
return {sim.directory for sim in query}
|
||||
|
||||
|
||||
def clean_leaves():
|
||||
"""Delete objects with missing foreign key from the database."""
|
||||
session = Session()
|
||||
|
||||
|
||||
for cls in (StringAttribute, FloatAttribute):
|
||||
session.query(cls).filter(cls.simulation_id == None).delete()
|
||||
session.query(Parameter).filter(Parameter.evaluation_id == None).delete()
|
||||
# TODO: Delete evaluation leaves, requires joint query with parameter
|
||||
|
||||
session.commit()
|
||||
session.close()
|
||||
|
||||
def dump_db(dbfile, user=None, **kwargs):
|
||||
"""
|
||||
Dump the database into a new databse.
|
||||
|
||||
Args:
|
||||
dbfile: File descriptor of the new database.
|
||||
user (opt.): If None, the database of the current user is dumped.
|
||||
**kwargs: Any keyword arguments are passed to query_simulation
|
||||
"""
|
||||
if user is None:
|
||||
user = os.getlogin()
|
||||
if '://' not in dbfile:
|
||||
dbfile = 'sqlite:///' + dbfile
|
||||
dump_engine = sql.create_engine(dbfile)
|
||||
Base.metadata.create_all(dump_engine)
|
||||
dump_session = sql.orm.sessionmaker(bind=dump_engine)()
|
||||
for sim in query_simulation(user=user, **kwargs):
|
||||
dump_sim = sim.copy()
|
||||
for ev in sim.evaluations:
|
||||
dump_ev = ev.copy(simulation=dump_sim)
|
||||
dump_session.add(dump_ev)
|
||||
dump_session.commit()
|
||||
|
||||
|
||||
def dump_cli(args=None):
|
||||
"""Command line interface to dump the database to a file."""
|
||||
parser = argparse.ArgumentParser(description='CLI tool to create a databse dump.')
|
||||
|
||||
parser.add_argument('dbfile', help='The database file for the dump.')
|
||||
parser.add_argument(
|
||||
'--user', '-u',
|
||||
help='The user for which the database is dumped, default is the current user.'
|
||||
)
|
||||
args = parser.parse_args()
|
||||
dump_db(args.dbfile, user=args.user)
|
||||
|
||||
|
||||
def delete_dirs(dirpattern):
|
||||
session = Session()
|
||||
|
||||
simulations = query_simulation(directory=dirpattern, session=session)
|
||||
for sim in simulations:
|
||||
sim.delete(session=session)
|
||||
session.commit()
|
||||
session.close()
|
224
store/utils.py
Executable file
224
store/utils.py
Executable file
@ -0,0 +1,224 @@
|
||||
import os
|
||||
from numbers import Number
|
||||
from collections.abc import Iterable
|
||||
from functools import wraps
|
||||
import inspect
|
||||
from glob import glob
|
||||
import warnings
|
||||
import pandas as pd
|
||||
import numpy as np
|
||||
import traceback
|
||||
|
||||
try:
|
||||
import mdevaluate as md
|
||||
except ImportError:
|
||||
pass
|
||||
|
||||
from . import config
|
||||
|
||||
|
||||
def nice_systems(df):
|
||||
return df.replace(['.*bulk_3_1', '.*bulk_1_3', '.*bulk_1_9', '.*bulk'], ['3:1', '1:3', '1:9', '1:1'], regex=True)
|
||||
|
||||
|
||||
def numlike(x):
|
||||
return isinstance(x, Number)
|
||||
|
||||
|
||||
def number_shorthand(x):
|
||||
if numlike(x):
|
||||
return True
|
||||
elif isinstance(x, str):
|
||||
limits = x.split('-')
|
||||
if len(limits) is 2:
|
||||
try:
|
||||
limits = [float(a) for a in limits]
|
||||
except:
|
||||
return False
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
elif isinstance(x, Iterable):
|
||||
return all(numlike(v) for v in x)
|
||||
else:
|
||||
False
|
||||
|
||||
|
||||
def lazy_eq(a, b):
|
||||
try:
|
||||
return a == b
|
||||
except (ValueError, TypeError):
|
||||
return False
|
||||
|
||||
|
||||
def data_frame(**kwargs):
|
||||
try:
|
||||
df = pd.DataFrame(kwargs)
|
||||
except ValueError:
|
||||
df = pd.DataFrame(kwargs, index=[0])
|
||||
return df
|
||||
|
||||
|
||||
def traj_slice(N, skip, nr_averages):
|
||||
step = int(N * (1 - skip) // nr_averages) or 1
|
||||
return slice(int(skip * N), N, step)
|
||||
|
||||
|
||||
def set_correlation_defaults(kwargs):
|
||||
"""Set some sensefull defaults for shifted correlation parameters."""
|
||||
for k in config['correlation'].keys():
|
||||
kwargs.setdefault(k, config['correlation'].getfloat(k))
|
||||
return kwargs
|
||||
|
||||
|
||||
def merge_timeframes(left, right, on='time'):
|
||||
"""Merge two dataframes with overlapping time scales."""
|
||||
merged = pd.merge(left, right, on=on, how='outer', indicator=True, suffixes=('_x', ''))
|
||||
res = pd.concat(
|
||||
(left, merged[left.columns][merged._merge == 'right_only']), ignore_index=True
|
||||
).sort_values(by=on).reset_index(drop=True)
|
||||
return res
|
||||
|
||||
|
||||
def open_sim(directory, maxcache=None):
|
||||
return md.open(
|
||||
directory, topology=config['eval']['topology'], trajectory=config['eval']['trajectory'],
|
||||
reindex=True, nojump=config['eval']['nojump']
|
||||
)
|
||||
|
||||
|
||||
def collect_short(func):
|
||||
"""
|
||||
Decorator to run an analysis function for the given trajectory and associated short simulations.
|
||||
|
||||
Args:
|
||||
short_subdir (opt.): Directory of short simulations, relative to the main trajectory file.
|
||||
|
||||
Decorated functions will be evaluate for the given trajecotory. Subsequently, this decorator will
|
||||
look for multiple simulations in subdirectories '../short/*' of the trajecotory file. The results
|
||||
for these simulations are then averaged and merged with the result of the original trajectory.
|
||||
|
||||
The simulations should be organized as follows, where the main trajectory, for which the function
|
||||
is called, is basedir/out/long.xtc. Results for short times are then obtained from the two trajectories
|
||||
located in basedir/short/100 and basedir/short/500.
|
||||
|
||||
basedir/
|
||||
topol.tpr
|
||||
out/
|
||||
long.xtc
|
||||
short/
|
||||
100/
|
||||
topol.tpr
|
||||
out/
|
||||
short.xtc
|
||||
500/
|
||||
topol.tpr
|
||||
out/
|
||||
short.xtc
|
||||
|
||||
"""
|
||||
@wraps(func)
|
||||
def wrapped(trajectory, *args, **kwargs):
|
||||
res = func(trajectory, *args, **kwargs)
|
||||
indices = trajectory.atom_subset.indices
|
||||
description = trajectory.description
|
||||
directory = os.path.dirname(trajectory.frames.filename)
|
||||
short_dir = os.path.abspath(os.path.join(directory, config['eval']['short_dir']))
|
||||
timestep = trajectory[1].time - trajectory[0].time
|
||||
|
||||
params = inspect.signature(func).parameters
|
||||
has_other = 'other' in params
|
||||
if has_other:
|
||||
args = list(args)
|
||||
other = args.pop(list(params).index('other') - 1)
|
||||
other_indices = other.atom_subset.indices
|
||||
other_description = other.description
|
||||
|
||||
|
||||
res_short = {}
|
||||
N = 0
|
||||
for sd in glob(short_dir):
|
||||
md.logger.debug(sd)
|
||||
try:
|
||||
traj = open_sim(sd)
|
||||
except FileNotFoundError:
|
||||
md.logger.info('Unale to load short simulation: %s', sd)
|
||||
continue
|
||||
if traj is None:
|
||||
print('sim=None')
|
||||
continue
|
||||
N += 1
|
||||
sim = traj.subset(indices=indices)
|
||||
sim.description = description
|
||||
if isinstance(trajectory, md.coordinates.CoordinatesMap):
|
||||
mode = trajectory.coordinates.mode
|
||||
if mode is not None:
|
||||
sim = getattr(sim, mode)
|
||||
sim = md.coordinates.CoordinatesMap(sim, trajectory.function)
|
||||
else:
|
||||
mode = trajectory.mode
|
||||
if mode is not None:
|
||||
sim = getattr(sim, mode)
|
||||
|
||||
if has_other:
|
||||
other_sim = traj.subset(indices=other_indices)
|
||||
other_sim.description = other_description
|
||||
if isinstance(other, md.coordinates.CoordinatesMap):
|
||||
mode = other.coordinates.mode
|
||||
if mode is not None:
|
||||
other_sim = getattr(other_sim, mode)
|
||||
other_sim = md.coordinates.CoordinatesMap(other_sim, other.function)
|
||||
else:
|
||||
mode = other.mode
|
||||
if mode is not None:
|
||||
other_sim = getattr(other_sim, mode)
|
||||
|
||||
short_kwargs = kwargs
|
||||
win = min(round(timestep / (sim[-1].time * 0.9), 3), 0.5)
|
||||
short_kwargs['window'] = win
|
||||
short_kwargs['skip'] = 0.01
|
||||
short_kwargs['segments'] = min(int((0.9 - win) * (len(sim) - 1)), 20)
|
||||
if has_other:
|
||||
sr = func(sim, other_sim, *args, **short_kwargs)
|
||||
else:
|
||||
sr = func(sim, *args, **short_kwargs)
|
||||
for key, val in sr.items():
|
||||
if isinstance(val, pd.DataFrame):
|
||||
if key in res_short:
|
||||
res_short[key] += val
|
||||
else:
|
||||
res_short[key] = val
|
||||
for key in res_short:
|
||||
res_short[key] /= N
|
||||
if len(res_short) != 0:
|
||||
res.update({key: merge_timeframes(sr, res[key]) for key, sr in res_short.items()})
|
||||
return res
|
||||
|
||||
return wrapped
|
||||
|
||||
|
||||
def enhanced_bins(x, y, k=3):
|
||||
"""
|
||||
Determine enhanced bins for some x and y data.
|
||||
|
||||
The binssize will be reduced where the derivative of y is steep. The k parameter controlls,
|
||||
how strong the binsize is influenced by the steepness of y.
|
||||
"""
|
||||
dy = np.absolute(np.diff(y))
|
||||
dx_max = np.diff(x).mean()
|
||||
xnew = [min(x)]
|
||||
while xnew[-1] < max(x):
|
||||
i = np.where(x > xnew[-1])[0][0]
|
||||
if i >= len(dy):
|
||||
break
|
||||
dx = dx_max / (1 + k * dy[i])
|
||||
xnew.append(xnew[-1] + dx)
|
||||
return np.array(xnew)
|
||||
|
||||
|
||||
def excess_entropy(r, gr, ρ=1):
|
||||
with warnings.catch_warnings():
|
||||
warnings.simplefilter('ignore', category=RuntimeWarning)
|
||||
y = (gr * np.log(gr) - (gr - 1)) * r**2
|
||||
y = np.nan_to_num(y)
|
||||
return -2 * np.pi * ρ * np.trapz(y, r)
|
2
store/webview/__init__.py
Normal file
2
store/webview/__init__.py
Normal file
@ -0,0 +1,2 @@
|
||||
|
||||
from .view import app
|
1
store/webview/settings.py
Normal file
1
store/webview/settings.py
Normal file
@ -0,0 +1 @@
|
||||
|
2
store/webview/settings_local.py
Normal file
2
store/webview/settings_local.py
Normal file
@ -0,0 +1,2 @@
|
||||
|
||||
DB_FILE = 'sqlite://///home/phd/Projects/store.db'
|
587
store/webview/static/bootstrap_v3/css/bootstrap-theme.css
vendored
Normal file
587
store/webview/static/bootstrap_v3/css/bootstrap-theme.css
vendored
Normal file
@ -0,0 +1,587 @@
|
||||
/*!
|
||||
* Bootstrap v3.3.7 (http://getbootstrap.com)
|
||||
* Copyright 2011-2016 Twitter, Inc.
|
||||
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
|
||||
*/
|
||||
.btn-default,
|
||||
.btn-primary,
|
||||
.btn-success,
|
||||
.btn-info,
|
||||
.btn-warning,
|
||||
.btn-danger {
|
||||
text-shadow: 0 -1px 0 rgba(0, 0, 0, .2);
|
||||
-webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
|
||||
box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
|
||||
}
|
||||
.btn-default:active,
|
||||
.btn-primary:active,
|
||||
.btn-success:active,
|
||||
.btn-info:active,
|
||||
.btn-warning:active,
|
||||
.btn-danger:active,
|
||||
.btn-default.active,
|
||||
.btn-primary.active,
|
||||
.btn-success.active,
|
||||
.btn-info.active,
|
||||
.btn-warning.active,
|
||||
.btn-danger.active {
|
||||
-webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
|
||||
box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
|
||||
}
|
||||
.btn-default.disabled,
|
||||
.btn-primary.disabled,
|
||||
.btn-success.disabled,
|
||||
.btn-info.disabled,
|
||||
.btn-warning.disabled,
|
||||
.btn-danger.disabled,
|
||||
.btn-default[disabled],
|
||||
.btn-primary[disabled],
|
||||
.btn-success[disabled],
|
||||
.btn-info[disabled],
|
||||
.btn-warning[disabled],
|
||||
.btn-danger[disabled],
|
||||
fieldset[disabled] .btn-default,
|
||||
fieldset[disabled] .btn-primary,
|
||||
fieldset[disabled] .btn-success,
|
||||
fieldset[disabled] .btn-info,
|
||||
fieldset[disabled] .btn-warning,
|
||||
fieldset[disabled] .btn-danger {
|
||||
-webkit-box-shadow: none;
|
||||
box-shadow: none;
|
||||
}
|
||||
.btn-default .badge,
|
||||
.btn-primary .badge,
|
||||
.btn-success .badge,
|
||||
.btn-info .badge,
|
||||
.btn-warning .badge,
|
||||
.btn-danger .badge {
|
||||
text-shadow: none;
|
||||
}
|
||||
.btn:active,
|
||||
.btn.active {
|
||||
background-image: none;
|
||||
}
|
||||
.btn-default {
|
||||
text-shadow: 0 1px 0 #fff;
|
||||
background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%);
|
||||
background-image: -o-linear-gradient(top, #fff 0%, #e0e0e0 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#e0e0e0));
|
||||
background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #dbdbdb;
|
||||
border-color: #ccc;
|
||||
}
|
||||
.btn-default:hover,
|
||||
.btn-default:focus {
|
||||
background-color: #e0e0e0;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-default:active,
|
||||
.btn-default.active {
|
||||
background-color: #e0e0e0;
|
||||
border-color: #dbdbdb;
|
||||
}
|
||||
.btn-default.disabled,
|
||||
.btn-default[disabled],
|
||||
fieldset[disabled] .btn-default,
|
||||
.btn-default.disabled:hover,
|
||||
.btn-default[disabled]:hover,
|
||||
fieldset[disabled] .btn-default:hover,
|
||||
.btn-default.disabled:focus,
|
||||
.btn-default[disabled]:focus,
|
||||
fieldset[disabled] .btn-default:focus,
|
||||
.btn-default.disabled.focus,
|
||||
.btn-default[disabled].focus,
|
||||
fieldset[disabled] .btn-default.focus,
|
||||
.btn-default.disabled:active,
|
||||
.btn-default[disabled]:active,
|
||||
fieldset[disabled] .btn-default:active,
|
||||
.btn-default.disabled.active,
|
||||
.btn-default[disabled].active,
|
||||
fieldset[disabled] .btn-default.active {
|
||||
background-color: #e0e0e0;
|
||||
background-image: none;
|
||||
}
|
||||
.btn-primary {
|
||||
background-image: -webkit-linear-gradient(top, #337ab7 0%, #265a88 100%);
|
||||
background-image: -o-linear-gradient(top, #337ab7 0%, #265a88 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#265a88));
|
||||
background-image: linear-gradient(to bottom, #337ab7 0%, #265a88 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff265a88', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #245580;
|
||||
}
|
||||
.btn-primary:hover,
|
||||
.btn-primary:focus {
|
||||
background-color: #265a88;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-primary:active,
|
||||
.btn-primary.active {
|
||||
background-color: #265a88;
|
||||
border-color: #245580;
|
||||
}
|
||||
.btn-primary.disabled,
|
||||
.btn-primary[disabled],
|
||||
fieldset[disabled] .btn-primary,
|
||||
.btn-primary.disabled:hover,
|
||||
.btn-primary[disabled]:hover,
|
||||
fieldset[disabled] .btn-primary:hover,
|
||||
.btn-primary.disabled:focus,
|
||||
.btn-primary[disabled]:focus,
|
||||
fieldset[disabled] .btn-primary:focus,
|
||||
.btn-primary.disabled.focus,
|
||||
.btn-primary[disabled].focus,
|
||||
fieldset[disabled] .btn-primary.focus,
|
||||
.btn-primary.disabled:active,
|
||||
.btn-primary[disabled]:active,
|
||||
fieldset[disabled] .btn-primary:active,
|
||||
.btn-primary.disabled.active,
|
||||
.btn-primary[disabled].active,
|
||||
fieldset[disabled] .btn-primary.active {
|
||||
background-color: #265a88;
|
||||
background-image: none;
|
||||
}
|
||||
.btn-success {
|
||||
background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%);
|
||||
background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641));
|
||||
background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #3e8f3e;
|
||||
}
|
||||
.btn-success:hover,
|
||||
.btn-success:focus {
|
||||
background-color: #419641;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-success:active,
|
||||
.btn-success.active {
|
||||
background-color: #419641;
|
||||
border-color: #3e8f3e;
|
||||
}
|
||||
.btn-success.disabled,
|
||||
.btn-success[disabled],
|
||||
fieldset[disabled] .btn-success,
|
||||
.btn-success.disabled:hover,
|
||||
.btn-success[disabled]:hover,
|
||||
fieldset[disabled] .btn-success:hover,
|
||||
.btn-success.disabled:focus,
|
||||
.btn-success[disabled]:focus,
|
||||
fieldset[disabled] .btn-success:focus,
|
||||
.btn-success.disabled.focus,
|
||||
.btn-success[disabled].focus,
|
||||
fieldset[disabled] .btn-success.focus,
|
||||
.btn-success.disabled:active,
|
||||
.btn-success[disabled]:active,
|
||||
fieldset[disabled] .btn-success:active,
|
||||
.btn-success.disabled.active,
|
||||
.btn-success[disabled].active,
|
||||
fieldset[disabled] .btn-success.active {
|
||||
background-color: #419641;
|
||||
background-image: none;
|
||||
}
|
||||
.btn-info {
|
||||
background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
|
||||
background-image: -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#2aabd2));
|
||||
background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #28a4c9;
|
||||
}
|
||||
.btn-info:hover,
|
||||
.btn-info:focus {
|
||||
background-color: #2aabd2;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-info:active,
|
||||
.btn-info.active {
|
||||
background-color: #2aabd2;
|
||||
border-color: #28a4c9;
|
||||
}
|
||||
.btn-info.disabled,
|
||||
.btn-info[disabled],
|
||||
fieldset[disabled] .btn-info,
|
||||
.btn-info.disabled:hover,
|
||||
.btn-info[disabled]:hover,
|
||||
fieldset[disabled] .btn-info:hover,
|
||||
.btn-info.disabled:focus,
|
||||
.btn-info[disabled]:focus,
|
||||
fieldset[disabled] .btn-info:focus,
|
||||
.btn-info.disabled.focus,
|
||||
.btn-info[disabled].focus,
|
||||
fieldset[disabled] .btn-info.focus,
|
||||
.btn-info.disabled:active,
|
||||
.btn-info[disabled]:active,
|
||||
fieldset[disabled] .btn-info:active,
|
||||
.btn-info.disabled.active,
|
||||
.btn-info[disabled].active,
|
||||
fieldset[disabled] .btn-info.active {
|
||||
background-color: #2aabd2;
|
||||
background-image: none;
|
||||
}
|
||||
.btn-warning {
|
||||
background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
|
||||
background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316));
|
||||
background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #e38d13;
|
||||
}
|
||||
.btn-warning:hover,
|
||||
.btn-warning:focus {
|
||||
background-color: #eb9316;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-warning:active,
|
||||
.btn-warning.active {
|
||||
background-color: #eb9316;
|
||||
border-color: #e38d13;
|
||||
}
|
||||
.btn-warning.disabled,
|
||||
.btn-warning[disabled],
|
||||
fieldset[disabled] .btn-warning,
|
||||
.btn-warning.disabled:hover,
|
||||
.btn-warning[disabled]:hover,
|
||||
fieldset[disabled] .btn-warning:hover,
|
||||
.btn-warning.disabled:focus,
|
||||
.btn-warning[disabled]:focus,
|
||||
fieldset[disabled] .btn-warning:focus,
|
||||
.btn-warning.disabled.focus,
|
||||
.btn-warning[disabled].focus,
|
||||
fieldset[disabled] .btn-warning.focus,
|
||||
.btn-warning.disabled:active,
|
||||
.btn-warning[disabled]:active,
|
||||
fieldset[disabled] .btn-warning:active,
|
||||
.btn-warning.disabled.active,
|
||||
.btn-warning[disabled].active,
|
||||
fieldset[disabled] .btn-warning.active {
|
||||
background-color: #eb9316;
|
||||
background-image: none;
|
||||
}
|
||||
.btn-danger {
|
||||
background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
|
||||
background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a));
|
||||
background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #b92c28;
|
||||
}
|
||||
.btn-danger:hover,
|
||||
.btn-danger:focus {
|
||||
background-color: #c12e2a;
|
||||
background-position: 0 -15px;
|
||||
}
|
||||
.btn-danger:active,
|
||||
.btn-danger.active {
|
||||
background-color: #c12e2a;
|
||||
border-color: #b92c28;
|
||||
}
|
||||
.btn-danger.disabled,
|
||||
.btn-danger[disabled],
|
||||
fieldset[disabled] .btn-danger,
|
||||
.btn-danger.disabled:hover,
|
||||
.btn-danger[disabled]:hover,
|
||||
fieldset[disabled] .btn-danger:hover,
|
||||
.btn-danger.disabled:focus,
|
||||
.btn-danger[disabled]:focus,
|
||||
fieldset[disabled] .btn-danger:focus,
|
||||
.btn-danger.disabled.focus,
|
||||
.btn-danger[disabled].focus,
|
||||
fieldset[disabled] .btn-danger.focus,
|
||||
.btn-danger.disabled:active,
|
||||
.btn-danger[disabled]:active,
|
||||
fieldset[disabled] .btn-danger:active,
|
||||
.btn-danger.disabled.active,
|
||||
.btn-danger[disabled].active,
|
||||
fieldset[disabled] .btn-danger.active {
|
||||
background-color: #c12e2a;
|
||||
background-image: none;
|
||||
}
|
||||
.thumbnail,
|
||||
.img-thumbnail {
|
||||
-webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
|
||||
box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
|
||||
}
|
||||
.dropdown-menu > li > a:hover,
|
||||
.dropdown-menu > li > a:focus {
|
||||
background-color: #e8e8e8;
|
||||
background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
|
||||
background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8));
|
||||
background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
}
|
||||
.dropdown-menu > .active > a,
|
||||
.dropdown-menu > .active > a:hover,
|
||||
.dropdown-menu > .active > a:focus {
|
||||
background-color: #2e6da4;
|
||||
background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
|
||||
background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4));
|
||||
background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
}
|
||||
.navbar-default {
|
||||
background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%);
|
||||
background-image: -o-linear-gradient(top, #fff 0%, #f8f8f8 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8));
|
||||
background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-radius: 4px;
|
||||
-webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
|
||||
box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
|
||||
}
|
||||
.navbar-default .navbar-nav > .open > a,
|
||||
.navbar-default .navbar-nav > .active > a {
|
||||
background-image: -webkit-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%);
|
||||
background-image: -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#dbdbdb), to(#e2e2e2));
|
||||
background-image: linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdbdbdb', endColorstr='#ffe2e2e2', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
-webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
|
||||
box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
|
||||
}
|
||||
.navbar-brand,
|
||||
.navbar-nav > li > a {
|
||||
text-shadow: 0 1px 0 rgba(255, 255, 255, .25);
|
||||
}
|
||||
.navbar-inverse {
|
||||
background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%);
|
||||
background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222));
|
||||
background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
|
||||
background-repeat: repeat-x;
|
||||
border-radius: 4px;
|
||||
}
|
||||
.navbar-inverse .navbar-nav > .open > a,
|
||||
.navbar-inverse .navbar-nav > .active > a {
|
||||
background-image: -webkit-linear-gradient(top, #080808 0%, #0f0f0f 100%);
|
||||
background-image: -o-linear-gradient(top, #080808 0%, #0f0f0f 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#080808), to(#0f0f0f));
|
||||
background-image: linear-gradient(to bottom, #080808 0%, #0f0f0f 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff080808', endColorstr='#ff0f0f0f', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
-webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
|
||||
box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
|
||||
}
|
||||
.navbar-inverse .navbar-brand,
|
||||
.navbar-inverse .navbar-nav > li > a {
|
||||
text-shadow: 0 -1px 0 rgba(0, 0, 0, .25);
|
||||
}
|
||||
.navbar-static-top,
|
||||
.navbar-fixed-top,
|
||||
.navbar-fixed-bottom {
|
||||
border-radius: 0;
|
||||
}
|
||||
@media (max-width: 767px) {
|
||||
.navbar .navbar-nav .open .dropdown-menu > .active > a,
|
||||
.navbar .navbar-nav .open .dropdown-menu > .active > a:hover,
|
||||
.navbar .navbar-nav .open .dropdown-menu > .active > a:focus {
|
||||
color: #fff;
|
||||
background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
|
||||
background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4));
|
||||
background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
}
|
||||
}
|
||||
.alert {
|
||||
text-shadow: 0 1px 0 rgba(255, 255, 255, .2);
|
||||
-webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
|
||||
box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
|
||||
}
|
||||
.alert-success {
|
||||
background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
|
||||
background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc));
|
||||
background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #b2dba1;
|
||||
}
|
||||
.alert-info {
|
||||
background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
|
||||
background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0));
|
||||
background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #9acfea;
|
||||
}
|
||||
.alert-warning {
|
||||
background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
|
||||
background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0));
|
||||
background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #f5e79e;
|
||||
}
|
||||
.alert-danger {
|
||||
background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
|
||||
background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3));
|
||||
background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
border-color: #dca7a7;
|
||||
}
|
||||
.progress {
|
||||
background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
|
||||
background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5));
|
||||
background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
}
|
||||
.progress-bar {
|
||||
background-image: -webkit-linear-gradient(top, #337ab7 0%, #286090 100%);
|
||||
background-image: -o-linear-gradient(top, #337ab7 0%, #286090 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#286090));
|
||||
background-image: linear-gradient(to bottom, #337ab7 0%, #286090 100%);
|
||||
filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff286090', GradientType=0);
|
||||
background-repeat: repeat-x;
|
||||
}
|
||||
.progress-bar-success {
|
||||
background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%);
|
||||
background-image: -o-linear-gradient(top, #5cb85c 0%, #449d44 100%);
|
||||
background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#449d44));
|
||||
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After Width: | Height: | Size: 106 KiB |
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2377
store/webview/static/bootstrap_v3/js/bootstrap.js
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2377
store/webview/static/bootstrap_v3/js/bootstrap.js
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7
store/webview/static/bootstrap_v3/js/bootstrap.min.js
vendored
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7
store/webview/static/bootstrap_v3/js/bootstrap.min.js
vendored
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13
store/webview/static/bootstrap_v3/js/npm.js
Normal file
13
store/webview/static/bootstrap_v3/js/npm.js
Normal file
@ -0,0 +1,13 @@
|
||||
// This file is autogenerated via the `commonjs` Grunt task. You can require() this file in a CommonJS environment.
|
||||
require('../../js/transition.js')
|
||||
require('../../js/alert.js')
|
||||
require('../../js/button.js')
|
||||
require('../../js/carousel.js')
|
||||
require('../../js/collapse.js')
|
||||
require('../../js/dropdown.js')
|
||||
require('../../js/modal.js')
|
||||
require('../../js/tooltip.js')
|
||||
require('../../js/popover.js')
|
||||
require('../../js/scrollspy.js')
|
||||
require('../../js/tab.js')
|
||||
require('../../js/affix.js')
|
2050
store/webview/static/bootstrap_v4/css/bootstrap-grid.css
vendored
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2050
store/webview/static/bootstrap_v4/css/bootstrap-grid.css
vendored
Normal file
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7
store/webview/static/bootstrap_v4/css/bootstrap-grid.min.css
vendored
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7
store/webview/static/bootstrap_v4/css/bootstrap-grid.min.css
vendored
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330
store/webview/static/bootstrap_v4/css/bootstrap-reboot.css
vendored
Normal file
330
store/webview/static/bootstrap_v4/css/bootstrap-reboot.css
vendored
Normal file
@ -0,0 +1,330 @@
|
||||
/*!
|
||||
* Bootstrap Reboot v4.0.0 (https://getbootstrap.com)
|
||||
* Copyright 2011-2018 The Bootstrap Authors
|
||||
* Copyright 2011-2018 Twitter, Inc.
|
||||
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
|
||||
* Forked from Normalize.css, licensed MIT (https://github.com/necolas/normalize.css/blob/master/LICENSE.md)
|
||||
*/
|
||||
*,
|
||||
*::before,
|
||||
*::after {
|
||||
box-sizing: border-box;
|
||||
}
|
||||
|
||||
html {
|
||||
font-family: sans-serif;
|
||||
line-height: 1.15;
|
||||
-webkit-text-size-adjust: 100%;
|
||||
-ms-text-size-adjust: 100%;
|
||||
-ms-overflow-style: scrollbar;
|
||||
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|
||||
}
|
||||
|
||||
@-ms-viewport {
|
||||
width: device-width;
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||||
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|
||||
|
||||
article, aside, dialog, figcaption, figure, footer, header, hgroup, main, nav, section {
|
||||
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|
||||
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|
||||
|
||||
body {
|
||||
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|
||||
font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
|
||||
font-size: 1rem;
|
||||
font-weight: 400;
|
||||
line-height: 1.5;
|
||||
color: #212529;
|
||||
text-align: left;
|
||||
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|
||||
}
|
||||
|
||||
[tabindex="-1"]:focus {
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||||
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||||
}
|
||||
|
||||
hr {
|
||||
box-sizing: content-box;
|
||||
height: 0;
|
||||
overflow: visible;
|
||||
}
|
||||
|
||||
h1, h2, h3, h4, h5, h6 {
|
||||
margin-top: 0;
|
||||
margin-bottom: 0.5rem;
|
||||
}
|
||||
|
||||
p {
|
||||
margin-top: 0;
|
||||
margin-bottom: 1rem;
|
||||
}
|
||||
|
||||
abbr[title],
|
||||
abbr[data-original-title] {
|
||||
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|
||||
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|
||||
text-decoration: underline dotted;
|
||||
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||||
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|
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|
||||
|
||||
address {
|
||||
margin-bottom: 1rem;
|
||||
font-style: normal;
|
||||
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|
||||
}
|
||||
|
||||
ol,
|
||||
ul,
|
||||
dl {
|
||||
margin-top: 0;
|
||||
margin-bottom: 1rem;
|
||||
}
|
||||
|
||||
ol ol,
|
||||
ul ul,
|
||||
ol ul,
|
||||
ul ol {
|
||||
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|
||||
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|
||||
|
||||
dt {
|
||||
font-weight: 700;
|
||||
}
|
||||
|
||||
dd {
|
||||
margin-bottom: .5rem;
|
||||
margin-left: 0;
|
||||
}
|
||||
|
||||
blockquote {
|
||||
margin: 0 0 1rem;
|
||||
}
|
||||
|
||||
dfn {
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
b,
|
||||
strong {
|
||||
font-weight: bolder;
|
||||
}
|
||||
|
||||
small {
|
||||
font-size: 80%;
|
||||
}
|
||||
|
||||
sub,
|
||||
sup {
|
||||
position: relative;
|
||||
font-size: 75%;
|
||||
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|
||||
vertical-align: baseline;
|
||||
}
|
||||
|
||||
sub {
|
||||
bottom: -.25em;
|
||||
}
|
||||
|
||||
sup {
|
||||
top: -.5em;
|
||||
}
|
||||
|
||||
a {
|
||||
color: #007bff;
|
||||
text-decoration: none;
|
||||
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|
||||
-webkit-text-decoration-skip: objects;
|
||||
}
|
||||
|
||||
a:hover {
|
||||
color: #0056b3;
|
||||
text-decoration: underline;
|
||||
}
|
||||
|
||||
a:not([href]):not([tabindex]) {
|
||||
color: inherit;
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
a:not([href]):not([tabindex]):hover, a:not([href]):not([tabindex]):focus {
|
||||
color: inherit;
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
a:not([href]):not([tabindex]):focus {
|
||||
outline: 0;
|
||||
}
|
||||
|
||||
pre,
|
||||
code,
|
||||
kbd,
|
||||
samp {
|
||||
font-family: monospace, monospace;
|
||||
font-size: 1em;
|
||||
}
|
||||
|
||||
pre {
|
||||
margin-top: 0;
|
||||
margin-bottom: 1rem;
|
||||
overflow: auto;
|
||||
-ms-overflow-style: scrollbar;
|
||||
}
|
||||
|
||||
figure {
|
||||
margin: 0 0 1rem;
|
||||
}
|
||||
|
||||
img {
|
||||
vertical-align: middle;
|
||||
border-style: none;
|
||||
}
|
||||
|
||||
svg:not(:root) {
|
||||
overflow: hidden;
|
||||
}
|
||||
|
||||
table {
|
||||
border-collapse: collapse;
|
||||
}
|
||||
|
||||
caption {
|
||||
padding-top: 0.75rem;
|
||||
padding-bottom: 0.75rem;
|
||||
color: #6c757d;
|
||||
text-align: left;
|
||||
caption-side: bottom;
|
||||
}
|
||||
|
||||
th {
|
||||
text-align: inherit;
|
||||
}
|
||||
|
||||
label {
|
||||
display: inline-block;
|
||||
margin-bottom: .5rem;
|
||||
}
|
||||
|
||||
button {
|
||||
border-radius: 0;
|
||||
}
|
||||
|
||||
button:focus {
|
||||
outline: 1px dotted;
|
||||
outline: 5px auto -webkit-focus-ring-color;
|
||||
}
|
||||
|
||||
input,
|
||||
button,
|
||||
select,
|
||||
optgroup,
|
||||
textarea {
|
||||
margin: 0;
|
||||
font-family: inherit;
|
||||
font-size: inherit;
|
||||
line-height: inherit;
|
||||
}
|
||||
|
||||
button,
|
||||
input {
|
||||
overflow: visible;
|
||||
}
|
||||
|
||||
button,
|
||||
select {
|
||||
text-transform: none;
|
||||
}
|
||||
|
||||
button,
|
||||
html [type="button"],
|
||||
[type="reset"],
|
||||
[type="submit"] {
|
||||
-webkit-appearance: button;
|
||||
}
|
||||
|
||||
button::-moz-focus-inner,
|
||||
[type="button"]::-moz-focus-inner,
|
||||
[type="reset"]::-moz-focus-inner,
|
||||
[type="submit"]::-moz-focus-inner {
|
||||
padding: 0;
|
||||
border-style: none;
|
||||
}
|
||||
|
||||
input[type="radio"],
|
||||
input[type="checkbox"] {
|
||||
box-sizing: border-box;
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
input[type="date"],
|
||||
input[type="time"],
|
||||
input[type="datetime-local"],
|
||||
input[type="month"] {
|
||||
-webkit-appearance: listbox;
|
||||
}
|
||||
|
||||
textarea {
|
||||
overflow: auto;
|
||||
resize: vertical;
|
||||
}
|
||||
|
||||
fieldset {
|
||||
min-width: 0;
|
||||
padding: 0;
|
||||
margin: 0;
|
||||
border: 0;
|
||||
}
|
||||
|
||||
legend {
|
||||
display: block;
|
||||
width: 100%;
|
||||
max-width: 100%;
|
||||
padding: 0;
|
||||
margin-bottom: .5rem;
|
||||
font-size: 1.5rem;
|
||||
line-height: inherit;
|
||||
color: inherit;
|
||||
white-space: normal;
|
||||
}
|
||||
|
||||
progress {
|
||||
vertical-align: baseline;
|
||||
}
|
||||
|
||||
[type="number"]::-webkit-inner-spin-button,
|
||||
[type="number"]::-webkit-outer-spin-button {
|
||||
height: auto;
|
||||
}
|
||||
|
||||
[type="search"] {
|
||||
outline-offset: -2px;
|
||||
-webkit-appearance: none;
|
||||
}
|
||||
|
||||
[type="search"]::-webkit-search-cancel-button,
|
||||
[type="search"]::-webkit-search-decoration {
|
||||
-webkit-appearance: none;
|
||||
}
|
||||
|
||||
::-webkit-file-upload-button {
|
||||
font: inherit;
|
||||
-webkit-appearance: button;
|
||||
}
|
||||
|
||||
output {
|
||||
display: inline-block;
|
||||
}
|
||||
|
||||
summary {
|
||||
display: list-item;
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
template {
|
||||
display: none;
|
||||
}
|
||||
|
||||
[hidden] {
|
||||
display: none !important;
|
||||
}
|
||||
/*# sourceMappingURL=bootstrap-reboot.css.map */
|
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8
store/webview/static/bootstrap_v4/css/bootstrap-reboot.min.css
vendored
Normal file
8
store/webview/static/bootstrap_v4/css/bootstrap-reboot.min.css
vendored
Normal file
@ -0,0 +1,8 @@
|
||||
/*!
|
||||
* Bootstrap Reboot v4.0.0 (https://getbootstrap.com)
|
||||
* Copyright 2011-2018 The Bootstrap Authors
|
||||
* Copyright 2011-2018 Twitter, Inc.
|
||||
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
|
||||
* Forked from Normalize.css, licensed MIT (https://github.com/necolas/normalize.css/blob/master/LICENSE.md)
|
||||
*/*,::after,::before{box-sizing:border-box}html{font-family:sans-serif;line-height:1.15;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;-ms-overflow-style:scrollbar;-webkit-tap-highlight-color:transparent}@-ms-viewport{width:device-width}article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}body{margin:0;font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:1rem;font-weight:400;line-height:1.5;color:#212529;text-align:left;background-color:#fff}[tabindex="-1"]:focus{outline:0!important}hr{box-sizing:content-box;height:0;overflow:visible}h1,h2,h3,h4,h5,h6{margin-top:0;margin-bottom:.5rem}p{margin-top:0;margin-bottom:1rem}abbr[data-original-title],abbr[title]{text-decoration:underline;-webkit-text-decoration:underline dotted;text-decoration:underline dotted;cursor:help;border-bottom:0}address{margin-bottom:1rem;font-style:normal;line-height:inherit}dl,ol,ul{margin-top:0;margin-bottom:1rem}ol ol,ol ul,ul ol,ul ul{margin-bottom:0}dt{font-weight:700}dd{margin-bottom:.5rem;margin-left:0}blockquote{margin:0 0 1rem}dfn{font-style:italic}b,strong{font-weight:bolder}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sub{bottom:-.25em}sup{top:-.5em}a{color:#007bff;text-decoration:none;background-color:transparent;-webkit-text-decoration-skip:objects}a:hover{color:#0056b3;text-decoration:underline}a:not([href]):not([tabindex]){color:inherit;text-decoration:none}a:not([href]):not([tabindex]):focus,a:not([href]):not([tabindex]):hover{color:inherit;text-decoration:none}a:not([href]):not([tabindex]):focus{outline:0}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}pre{margin-top:0;margin-bottom:1rem;overflow:auto;-ms-overflow-style:scrollbar}figure{margin:0 0 1rem}img{vertical-align:middle;border-style:none}svg:not(:root){overflow:hidden}table{border-collapse:collapse}caption{padding-top:.75rem;padding-bottom:.75rem;color:#6c757d;text-align:left;caption-side:bottom}th{text-align:inherit}label{display:inline-block;margin-bottom:.5rem}button{border-radius:0}button:focus{outline:1px dotted;outline:5px auto -webkit-focus-ring-color}button,input,optgroup,select,textarea{margin:0;font-family:inherit;font-size:inherit;line-height:inherit}button,input{overflow:visible}button,select{text-transform:none}[type=reset],[type=submit],button,html [type=button]{-webkit-appearance:button}[type=button]::-moz-focus-inner,[type=reset]::-moz-focus-inner,[type=submit]::-moz-focus-inner,button::-moz-focus-inner{padding:0;border-style:none}input[type=checkbox],input[type=radio]{box-sizing:border-box;padding:0}input[type=date],input[type=datetime-local],input[type=month],input[type=time]{-webkit-appearance:listbox}textarea{overflow:auto;resize:vertical}fieldset{min-width:0;padding:0;margin:0;border:0}legend{display:block;width:100%;max-width:100%;padding:0;margin-bottom:.5rem;font-size:1.5rem;line-height:inherit;color:inherit;white-space:normal}progress{vertical-align:baseline}[type=number]::-webkit-inner-spin-button,[type=number]::-webkit-outer-spin-button{height:auto}[type=search]{outline-offset:-2px;-webkit-appearance:none}[type=search]::-webkit-search-cancel-button,[type=search]::-webkit-search-decoration{-webkit-appearance:none}::-webkit-file-upload-button{font:inherit;-webkit-appearance:button}output{display:inline-block}summary{display:list-item;cursor:pointer}template{display:none}[hidden]{display:none!important}
|
||||
/*# sourceMappingURL=bootstrap-reboot.min.css.map */
|
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store/webview/static/bootstrap_v4/css/bootstrap.css
vendored
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vendored
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vendored
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7
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vendored
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vendored
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vendored
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vendored
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vendored
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vendored
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vendored
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7
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vendored
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vendored
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2
store/webview/static/jquery_v3/jquery-3.3.1.slim.min.js
vendored
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2
store/webview/static/jquery_v3/jquery-3.3.1.slim.min.js
vendored
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5
store/webview/static/popper_v1/popper.min.js
vendored
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5
store/webview/static/popper_v1/popper.min.js
vendored
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28
store/webview/templates/base.html
Executable file
28
store/webview/templates/base.html
Executable file
@ -0,0 +1,28 @@
|
||||
<!doctype html>
|
||||
<head>
|
||||
<title>Store Webview</title>
|
||||
|
||||
<script defer type='text/javascript' src="{{ url_for('static', filename='jquery_v3/jquery-3.3.1.slim.min.js') }}"></script>
|
||||
<script defer type='text/javascript' src="{{ url_for('static', filename='popper_v1/popper.min.js') }}"></script>
|
||||
<script defer type='text/javascript' src="{{ url_for('static', filename='bootstrap_v4/js/bootstrap.min.js') }}"></script>
|
||||
|
||||
<link rel="stylesheet" href="{{ url_for('static', filename='bootstrap_v4/css/bootstrap.min.css') }}" />
|
||||
|
||||
|
||||
{% block head %}{% endblock %}
|
||||
</head>
|
||||
<body>
|
||||
<div class=page>
|
||||
<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
|
||||
<a class="navbar-brand" href="{{ url_for('view_simulations') }}">Store</a>
|
||||
<a class="nav-link" href="{{ url_for('view_statistics') }}">Statistics</a>
|
||||
</nav>
|
||||
{% for message in get_flashed_messages() %}
|
||||
<div class=flash>{{ message }}</div>
|
||||
{% endfor %}
|
||||
<br />
|
||||
<div class="container-fluid">
|
||||
{% block body %}{% endblock %}
|
||||
</div>
|
||||
</div>
|
||||
</body>
|
58
store/webview/templates/evaluation-details.html
Normal file
58
store/webview/templates/evaluation-details.html
Normal file
@ -0,0 +1,58 @@
|
||||
{% extends "simulation-details.html" %}
|
||||
|
||||
{% block head %}
|
||||
<script src="https://d3js.org/d3.v3.min.js"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/vega/3.0.0-beta.31/vega.js"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/vega-lite/2.0.0-beta.3/vega-lite.js"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/vega-embed/3.0.0-beta.14/vega-embed.js"></script>
|
||||
{% endblock %}
|
||||
|
||||
{% block evaluation %}
|
||||
<ol class="breadcrumb">
|
||||
<li class="breadcrumb-item">
|
||||
<a href="{{ url_for('view_simulation', sim_id=simulation.id) }}">Evaluations</a>
|
||||
</li>
|
||||
<li class="breadcrumb-item active">{{ evaluation.observable }} </li>
|
||||
</ol>
|
||||
<div class="row">
|
||||
<div class="col-md-4">
|
||||
<table class="table table-striped">
|
||||
<th>Evaluation parameters</th><th></th>
|
||||
<tr>
|
||||
<td>Selection</td>
|
||||
<td>{{ evaluation.selection }}</td>
|
||||
</tr>
|
||||
{% for param in evaluation_params %}
|
||||
<tr>
|
||||
<td>{{ param.name }}</td>
|
||||
<td>{{ param.value }}</td>
|
||||
</tr>
|
||||
{% endfor %}
|
||||
</table>
|
||||
|
||||
<div id="vis"></div>
|
||||
<script type="text/javascript">
|
||||
var spec = "{{ url_for('get_evaluation_plot_spec', id=evaluation.id) }}";
|
||||
vega.embed('#vis', spec);
|
||||
</script>
|
||||
</div>
|
||||
<div class="col-md-4">
|
||||
{% if data.to_html %}
|
||||
<div class="card">
|
||||
<div class="card-header"><a data-toggle="collapse" href="#data-table">Data</a></div>
|
||||
<div id="data-table" class="card-collapse collapse">
|
||||
<div class="card-body">
|
||||
{{ data.to_html(index=False) | replace('dataframe', 'table table-sm table-bordered table-striped') | safe }}
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
{% else %}
|
||||
<table class='table'>
|
||||
<tr>
|
||||
<td>Value</td><td>{{ data }}</td>
|
||||
</tr>
|
||||
</table>
|
||||
{% endif %}
|
||||
</div>
|
||||
</div>
|
||||
{% endblock %}
|
53
store/webview/templates/simulation-details.html
Normal file
53
store/webview/templates/simulation-details.html
Normal file
@ -0,0 +1,53 @@
|
||||
{% extends "base.html" %}
|
||||
|
||||
{% block body %}
|
||||
<h2>Simulation Details</h2>
|
||||
<div class="row">
|
||||
<div class="col-md-4">
|
||||
<div class="card card-default">
|
||||
<div class="card-header">
|
||||
<div class="row">
|
||||
<div class="col-auto">
|
||||
<b>Directory</b>
|
||||
</div>
|
||||
<div class="col-auto">{{ simulation.directory }}</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="card-body">
|
||||
<table class="table">
|
||||
<tr>
|
||||
<th>Parameters</th><th></th>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>User</td>
|
||||
<td>{{ simulation.user }}</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>Temperature</td>
|
||||
<td>{{ simulation.temperature }}</td>
|
||||
</tr>
|
||||
{% for param in sim_params %}
|
||||
<tr>
|
||||
<td>{{ param.name }}</td>
|
||||
<td>{{ param.value }}</td>
|
||||
</tr>
|
||||
{% endfor %}
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-8">
|
||||
{% block evaluation %}
|
||||
<ol class="breadcrumb">
|
||||
<li class="breadcrumb-item active">Evaluations</li>
|
||||
</ol>
|
||||
{% for ev_id, obs, sel in evaluations %}
|
||||
<a class="btn btn-info" style="margin: .1em" href="{{ url_for('view_evaluation', id=ev_id )}}">
|
||||
{{ obs }} <span class="badge badge-light">{{ sel }}</span>
|
||||
</a>
|
||||
{% endfor %}
|
||||
{% endblock %}
|
||||
</div>
|
||||
</div>
|
||||
{% endblock %}
|
46
store/webview/templates/simulations.html
Normal file
46
store/webview/templates/simulations.html
Normal file
@ -0,0 +1,46 @@
|
||||
{% extends "base.html" %}
|
||||
|
||||
{% block body %}
|
||||
<div class="card card-default">
|
||||
<div class="card-header">
|
||||
<h2>Simulations</h2>
|
||||
<form class="row" method="get">
|
||||
<div class="col-md-2">
|
||||
<div class="input-group">
|
||||
<span class="input-group-addon"><span class="glyphicon glyphicon-user"></span></span>
|
||||
<input class="form-control" type="text" placeholder="user", name="user" value="{{ request.args.user }}">
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-4">
|
||||
<div class="input-group">
|
||||
<span class="input-group-addon"><span class="glyphicon glyphicon-folder-open"></span></span>
|
||||
<input class="form-control" type="text" placeholder="directory" name="directory" value="{{ request.args.directory}}">
|
||||
</div>
|
||||
</div>
|
||||
<div class="btn-group">
|
||||
<button type="submit" class="btn btn-primary">Reload</button>
|
||||
<button type="reset" name="button" class="btn btn-danger">Reset</button>
|
||||
</div>
|
||||
|
||||
|
||||
</form>
|
||||
|
||||
</div>
|
||||
<div class="card-body">
|
||||
<table class='table table-striped table-sm table-hover'>
|
||||
<tr>
|
||||
<th>#</th><th>User</th><th>Directory</th>
|
||||
</tr>
|
||||
<tbody>
|
||||
{% for sim in simulations %}
|
||||
<tr>
|
||||
<td>
|
||||
<a href="{{ url_for('view_simulation', sim_id=sim.id) }}">{{ sim.id }}</a>
|
||||
</td><td>{{ sim.user}}</td><td>{{ sim.directory }}</td>
|
||||
</tr>
|
||||
{% endfor %}
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
{% endblock %}
|
36
store/webview/templates/statistics.html
Normal file
36
store/webview/templates/statistics.html
Normal file
@ -0,0 +1,36 @@
|
||||
{% extends "base.html" %}
|
||||
|
||||
{% block body %}
|
||||
<h2>Statistics</h2>
|
||||
<div class="row">
|
||||
<div class="col-md-5">
|
||||
<div class="card">
|
||||
<div class="card-header">
|
||||
<h4>Table size</h4>
|
||||
</div>
|
||||
<div class="card-body">
|
||||
{{ total_stats.to_html(index=False) | replace('dataframe', 'table table-sm table-bordered table-hover') | safe }}
|
||||
</div>
|
||||
</div>
|
||||
<br />
|
||||
<div class="card">
|
||||
<div class="card-header">
|
||||
<h4>User data</h4>
|
||||
</div>
|
||||
<div class="card-body">
|
||||
{{ user_stats.to_html(index=False) | replace('dataframe', 'table table-sm table-bordered table-hover') | safe }}
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-6">
|
||||
<div class="card">
|
||||
<div class="card-header">
|
||||
<h4>Evaluation data</h4>
|
||||
</div>
|
||||
<div class="card-body">
|
||||
{{ eval_stats.to_html(index=False) | replace('dataframe', 'table table-sm table-bordered table-hover') | safe }}
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
{% endblock %}
|
204
store/webview/view.py
Executable file
204
store/webview/view.py
Executable file
@ -0,0 +1,204 @@
|
||||
from flask import Flask, render_template, request, url_for
|
||||
|
||||
|
||||
from numbers import Number
|
||||
# from datetime import datetime
|
||||
import pandas as pd
|
||||
import json
|
||||
|
||||
try:
|
||||
import altair
|
||||
_ALTAIR = True
|
||||
except ImportError:
|
||||
_ALTAIR = False
|
||||
|
||||
from .. import store
|
||||
|
||||
from . import settings
|
||||
|
||||
|
||||
def numlike(x):
|
||||
return isinstance(x, Number)
|
||||
|
||||
|
||||
session = store.Session()
|
||||
|
||||
app = Flask(__name__)
|
||||
app.config.from_object(settings)
|
||||
app.config.from_envvar('STOREVIEW_SETTINGS', silent=True)
|
||||
|
||||
if 'DB_FILE' in app.config:
|
||||
print('Setting DB_FILE:', app.config['DB_FILE'])
|
||||
store.DB_FILE = app.config['DB_FILE']
|
||||
|
||||
|
||||
def db_total_stats():
|
||||
session = store.Session()
|
||||
df = pd.DataFrame(
|
||||
session.execute("""
|
||||
SELECT relname AS "relation",
|
||||
pg_size_pretty(pg_total_relation_size(C.oid)) AS "total_size"
|
||||
FROM pg_class C
|
||||
LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
|
||||
WHERE nspname NOT IN ('pg_catalog', 'information_schema')
|
||||
AND C.relkind <> 'i'
|
||||
AND nspname !~ '^pg_toast'
|
||||
AND relname !~ 'id_seq'
|
||||
ORDER BY pg_total_relation_size(C.oid) DESC
|
||||
LIMIT 20;
|
||||
""").fetchall(), columns=['tabel name', 'total size']
|
||||
)
|
||||
session.close()
|
||||
return df
|
||||
|
||||
|
||||
def db_user_stats():
|
||||
session = store.Session()
|
||||
df = pd.DataFrame(
|
||||
session.execute("""
|
||||
SELECT simulations.user, COUNT(DISTINCT simulations),
|
||||
pg_size_pretty(SUM(pg_column_size(data))) as "data-size",
|
||||
pg_size_pretty(SUM(pg_column_size(data)) / COUNT(DISTINCT simulations)) as "size / sim"
|
||||
FROM evaluations
|
||||
JOIN simulations
|
||||
ON (simulations.id = evaluations.simulation_id)
|
||||
GROUP BY simulations.user
|
||||
ORDER BY count DESC;
|
||||
""").fetchall(), columns=['user', '# of simulations', 'total data', 'data per simulation']
|
||||
)
|
||||
session.close()
|
||||
return df
|
||||
|
||||
|
||||
def db_eval_stats():
|
||||
session = store.Session()
|
||||
df = pd.DataFrame(
|
||||
session.execute("""
|
||||
SELECT observable,
|
||||
pg_size_pretty(ROUND(AVG(pg_column_size(data)), 0)) as "size-avg",
|
||||
pg_size_pretty(ROUND(SUM(pg_column_size(data)), 0)) as "size-total",
|
||||
COUNT(*), AVG(pg_column_size(data)) as "size_bytes"
|
||||
FROM evaluations
|
||||
GROUP BY observable
|
||||
ORDER BY size_bytes DESC;
|
||||
""").fetchall(), columns=['observable', 'Avg. size', 'Total size', '# of evaluations', 'size_bytes']
|
||||
).drop('size_bytes', axis=1)
|
||||
session.close()
|
||||
return df[~df['Total size'].isnull()]
|
||||
|
||||
|
||||
@app.route('/')
|
||||
def view_simulations():
|
||||
session = store.Session()
|
||||
simulations = store.query_simulation(
|
||||
directory='%' + request.args.get('directory', '') + '%',
|
||||
user=request.args.get('user', '') + '%',
|
||||
session=session
|
||||
).all()
|
||||
r = render_template('simulations.html', simulations=simulations)
|
||||
session.close()
|
||||
return r
|
||||
|
||||
|
||||
@app.route('/statistics')
|
||||
def view_statistics():
|
||||
return render_template('statistics.html', user_stats=db_user_stats(),
|
||||
total_stats=db_total_stats(), eval_stats=db_eval_stats())
|
||||
|
||||
|
||||
@app.route('/simulation/<int:sim_id>')
|
||||
def view_simulation(sim_id):
|
||||
session = store.Session()
|
||||
simulation = store.query_simulation(session=session).filter(store.Simulation.id == sim_id).first()
|
||||
params = simulation.string_params + simulation.float_params
|
||||
evaluations = list(session.query(store.Evaluation).filter(
|
||||
store.Evaluation.simulation_id == simulation.id).order_by('observable').values(
|
||||
'id', 'observable', 'selection'
|
||||
)
|
||||
)
|
||||
r = render_template('simulation-details.html', simulation=simulation,
|
||||
sim_params=params, evaluations=evaluations)
|
||||
session.close()
|
||||
return r
|
||||
|
||||
@app.route('/evaluation/<int:id>')
|
||||
def view_evaluation(id):
|
||||
session = store.Session()
|
||||
evaluation = session.query(store.Evaluation).filter(store.Evaluation.id == id).first()
|
||||
df = evaluation.data
|
||||
if numlike(df):
|
||||
data = df
|
||||
elif df is not None:
|
||||
data_columns = list(df.columns)
|
||||
for col in ['directory', 'T', 'user', 'selection', 'system', 'ensemble']:
|
||||
if col in data_columns:
|
||||
data_columns.remove(col)
|
||||
data = df[data_columns]
|
||||
else:
|
||||
data = None
|
||||
simulation = evaluation.simulation
|
||||
sim_params = simulation.string_params + simulation.float_params
|
||||
r = render_template('evaluation-details.html', simulation=simulation, evaluation=evaluation,
|
||||
sim_params=sim_params, evaluation_params=evaluation.parameters, data=data)
|
||||
session.close()
|
||||
return r
|
||||
|
||||
|
||||
@app.route('/evaluation/<int:id>/data.csv')
|
||||
def get_evaluation_data(id):
|
||||
session = store.Session()
|
||||
evaluation = session.query(store.Evaluation).filter(store.Evaluation.id == id).first()
|
||||
df = evaluation.data
|
||||
if numlike(df):
|
||||
data = df
|
||||
else:
|
||||
data_columns = list(df.columns)
|
||||
for col in ['directory', 'T', 'user', 'selection', 'system', 'ensemble']:
|
||||
if col in data_columns:
|
||||
data_columns.remove(col)
|
||||
data = df[data_columns]
|
||||
session.close()
|
||||
return data.to_csv()
|
||||
|
||||
|
||||
@app.route('/evaluation/<int:id>/spec.json')
|
||||
def get_evaluation_plot_spec(id):
|
||||
session = store.Session()
|
||||
evaluation = session.query(store.Evaluation).filter(store.Evaluation.id == id).first()
|
||||
df = evaluation.data
|
||||
if numlike(df) or not _ALTAIR:
|
||||
return '{}'
|
||||
else:
|
||||
data_columns = list(df.columns)
|
||||
for col in ['directory', 'T', 'user', 'selection', 'system', 'ensemble']:
|
||||
if col in data_columns:
|
||||
data_columns.remove(col)
|
||||
plot_spec = {}
|
||||
x = y = None
|
||||
for col in ['time', 'radius', 'r']:
|
||||
if col in data_columns:
|
||||
ycol = data_columns[(data_columns.index(col) + 1) % 2]
|
||||
if col == 'time':
|
||||
x = altair.X(col + ':Q', scale=altair.Scale(type='log'))
|
||||
else:
|
||||
x = altair.X(col + ':Q')
|
||||
if ycol == 'msd':
|
||||
y = altair.Y(ycol + ':Q', scale=altair.Scale(type='log'))
|
||||
else:
|
||||
y = altair.Y(ycol + ':Q')
|
||||
|
||||
if x is None:
|
||||
xcol, ycol = data_columns[:2]
|
||||
x = altair.X(xcol + ':Q')
|
||||
y = altair.Y(ycol + ':Q')
|
||||
|
||||
ch = altair.Chart(
|
||||
url_for('get_evaluation_data', id=id),
|
||||
# data,
|
||||
width=300, height=200).mark_point().encode(
|
||||
x=x, y=y)
|
||||
plot_spec = ch.to_dict()
|
||||
plot_spec["$schema"] = "https://vega.github.io/schema/vega-lite/v1.json"
|
||||
json.codecs
|
||||
session.close()
|
||||
return json.dumps(plot_spec)
|
26
test/test_analyse.py
Normal file
26
test/test_analyse.py
Normal file
@ -0,0 +1,26 @@
|
||||
import os
|
||||
import pytest
|
||||
import numpy as np
|
||||
|
||||
import mdevaluate as md
|
||||
import store.eval as seval
|
||||
import store.analyse as sana
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def water_trajectory(request, scope='module'):
|
||||
dname = os.environ.get('STORE_TESTDATA', '/autohome/niels/Projects/mdevaluate/test/data/water')
|
||||
return md.open(dname)
|
||||
|
||||
|
||||
def test_oaf(water_trajectory):
|
||||
kwargs = {'segments': 10, 'window': 0.5}
|
||||
dipole = sana.water_dipole(water_trajectory)
|
||||
res_1 = sana.oaf(dipole, order=1, **kwargs)['F1'].cor.values
|
||||
res_2 = sana.oaf(dipole, order=2, **kwargs)['F2'].cor.values
|
||||
assert (res_2 <= res_1).all()
|
||||
|
||||
bonds = sana.water_OH_bonds(water_trajectory)
|
||||
res_1 = sana.oaf(bonds, order=1, **kwargs)['F1'].cor.values
|
||||
res_2 = sana.oaf(bonds, order=2, **kwargs)['F2'].cor.values
|
||||
assert (res_2 <= res_1).all()
|
Reference in New Issue
Block a user