132 lines
4.7 KiB
Python
132 lines
4.7 KiB
Python
"""
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@package pmsco.calculator
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abstract scattering program interface.
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this module declares the basic interface to scattering programs.
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for each scattering program (EDAC, MSC, SSC, ...) a specific interface must be derived from CalcInterface.
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the derived interface must implement the run() method.
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the run() method and the scattering code may use only the parameters declared in the interface.
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TestCalcInterface is provided for testing the PMSCO code quickly without calling an external program.
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@author Matthias Muntwiler
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@copyright (c) 2015 by Paul Scherrer Institut @n
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Licensed under the Apache License, Version 2.0 (the "License"); @n
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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"""
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import time
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import numpy as np
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import data as md
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import cluster as mc
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__author__ = 'matthias muntwiler'
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class Calculator(object):
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"""
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Interface class to the calculation program.
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"""
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def run(self, params, cluster, scan, output_file):
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"""
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run a calculation with the given parameters and cluster.
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the result is returned as the method result and in a file named <code>output_file + '.etpi'</code>,
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or <code>output_file + '.etpai'</code> depending on scan mode.
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all other intermediate files are deleted unless keep_temp_files is True.
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@param params: a msco_project.Params() object with all necessary values except cluster and output files set.
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@param cluster: a msco_cluster.Cluster() object with all atom positions set.
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@param scan: a msco_project.Scan() object describing the experimental scanning scheme.
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@param output_file: base name for all intermediate and output files
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@return: result_file, files_cats
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@arg result_file is the name of the main ETPI or ETPAI result file to be further processed.
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@arg files_cats is a dictionary that lists the names of all created data files with their category.
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the dictionary key is the file name,
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the value is the file category (cluster, phase, etc.).
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"""
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return None, None
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def check_cluster(self, cluster, output_file):
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"""
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export the cluster in XYZ format for reference.
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along with the complete cluster, the method also saves cuts in the xz (extension .y.xyz) and yz (.x.xyz) plane.
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@param cluster: a pmsco.cluster.Cluster() object with all atom positions set.
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@param output_file: base name for all intermediate and output files
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@return: dictionary listing the names of the created files with their category.
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the dictionary key is the file name,
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the value is the file category (cluster).
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@warning experimental: this method may be moved elsewhere in a future version.
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"""
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xyz_filename = output_file + ".xyz"
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cluster.save_to_file(xyz_filename, fmt=mc.FMT_XYZ)
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files = {xyz_filename: 'cluster'}
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clucut = mc.Cluster()
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clucut.copy_from(cluster)
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clucut.trim_slab("x", 0.0, 0.1)
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xyz_filename = output_file + ".x.xyz"
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clucut.save_to_file(xyz_filename, fmt=mc.FMT_XYZ)
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files[xyz_filename] = 'cluster'
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clucut.copy_from(cluster)
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clucut.trim_slab("y", 0.0, 0.1)
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xyz_filename = output_file + ".y.xyz"
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clucut.save_to_file(xyz_filename, fmt=mc.FMT_XYZ)
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files[xyz_filename] = 'cluster'
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return files
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class TestCalculator(Calculator):
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"""
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interface class producing random data for testing the MSCO code without calling an external program.
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"""
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def run(self, params, cluster, scan, output_file):
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"""
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produce a random test data set.
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the scan scheme is generated from the given parameters.
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the intensities are random values.
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@return: result_file, files_cats
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the result file contains an ETPI or ETPAI array with random intensity data.
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"""
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# set up scan
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params.fixed_cluster = 'a' in scan.mode
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# generate file names
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base_filename = output_file
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clu_filename = base_filename + ".clu"
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if params.fixed_cluster:
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etpi_filename = base_filename + ".etpai"
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else:
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etpi_filename = base_filename + ".etpi"
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cluster.save_to_file(clu_filename)
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# generate data and save in ETPI or ETPAI format
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result_etpi = scan.raw_data.copy()
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result_etpi['i'] = np.random.random_sample(result_etpi.shape)
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# slow down the test for debugging
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time.sleep(5)
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md.save_data(etpi_filename, result_etpi)
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files = {clu_filename: 'cluster', etpi_filename: 'energy'}
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return etpi_filename, files
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