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How to use converge method in molecule

Best Python code snippet using molecule_python

cases.py

Source:cases.py

...255    pgs[_(2)].connect(256        acts[_(2)],257        acts[_(3)],258        acts[_(4)]259    ).converge(cgs[_(1)]).extend(acts[_(7)]).extend(egs[_(1)]).connect(260        pgs[_(2)],261        cgs[_(3)]262    )263    acts[_(5)].extend(egs[_(7)]).connect(264        cgs[_(3)],265        acts[_(8)]266    ).to(acts[_(8)]).extend(egs[_(8)]).connect(267        acts[_(8)],268        acts[_(11)]269    ).to(acts[_(11)]).extend(cgs[_(3)])270    acts[_(6)].extend(egs[_(2)]).connect(271        acts[_(9)],272        acts[_(10)],273    ).converge(cgs[_(2)]).extend(acts[_(12)]).extend(egs[_(6)]).connect(274        acts[_(6)],275        cgs[_(3)],276        cgs[_(2)]277    ).to(egs[_(2)]).connect(acts[_(6)])278    cgs[_(3)].extend(acts[_(13)]).extend(egs[_(3)]).connect(279        end,280        acts[_(14)],281        pgs[_(3)],282        acts[_(1)]283    )284    acts[_(14)].extend(egs[_(4)]).connect(285        acts[_(13)],286        cgs[_(4)]287    )288    pgs[_(3)].connect(289        acts[_(15)],290        acts[_(16)],291        acts[_(17)]292    ).to(acts[_(15)]).extend(acts[_(18)]).extend(cgs[_(4)]) \293        .to(acts[_(17)]).extend(egs[_(5)]).connect(294        acts[_(19)],295        acts[_(20)]296    ).to(acts[_(19)]).extend(cgs[_(4)]).to(acts[_(20)]).extend(cgs[_(4)]) \297        .to(acts[_(16)]).extend(cgs[_(4)]).extend(end)298    for node in nodes:299        a = outgoing_assert[node.id]300        out = {out.id for out in node.outgoing}301        testcase.assertEqual(a['len'], len(node.outgoing),302                             msg='{id} actual: {a}, expect: {e}'.format(id=node.id, a=len(node.outgoing), e=a['len']))303        testcase.assertEqual(a['outgoing'], out,304                             msg='{id} actual: {a}, expect: {e}'.format(id=node.id, a=out, e=a['outgoing']))305    return build_tree(start), gateway_validation_assert, stream_assert306def flow_valid_edge_case_1():307    start = EmptyStartEvent(id=start_event_id)308    act_1 = ServiceActivity(id=act_id(1))309    act_2 = ServiceActivity(id=act_id(2))310    eg = ExclusiveGateway(id=exclusive_gw_id(1), conditions={311        0: '123',312        1: '456',313        2: '789'314    })315    act_3 = ServiceActivity(id=act_id(3))316    end = EmptyEndEvent(id=end_event_id)317    start.extend(act_1).extend(act_2).extend(eg).connect(318        act_1,319        act_2,320        act_3321    ).to(act_3).extend(end)322    return build_tree(start)323def flow_valid_edge_case_2():324    return {325        'activities': {326            'act_1': {'component': {'inputs': {}, 'code': None}, 'outgoing': '82b12b6aae533e55bdcc5bccfb014c2d',327                      'incoming': ['3fc89273786a36b8a6e7beac8301274d'], 'name': None, 'error_ignorable': False,328                      'type': 'ServiceActivity', 'id': 'act_1', 'optional': False},329            'act_2': {'component': {'inputs': {}, 'code': None}, 'outgoing': '3368add44347310eaef1f26f25909026',330                      'incoming': ['76caeed0e6053fea9db84a89f56a74a8'], 'name': None, 'error_ignorable': False,331                      'type': 'ServiceActivity', 'id': 'act_2', 'optional': False}},332        'end_event': {'type': 'EmptyEndEvent', 'outgoing': '', 'incoming': ['05f91b45a15b37d7b0c96d3ff94bff80'],333                      'id': 'end_event_id', 'name': None},334        'flows': {335            '27a9cdeaef623d37834ac6917d05eac5': {'is_default': False, 'source': 'start_event_id', 'target': 'pg_1',336                                                 'id': '27a9cdeaef623d37834ac6917d05eac5'},337            '82b12b6aae533e55bdcc5bccfb014c2d': {'is_default': False, 'source': 'act_1', 'target': 'cg_1',338                                                 'id': '82b12b6aae533e55bdcc5bccfb014c2d'},339            '3368add44347310eaef1f26f25909026': {'is_default': False, 'source': 'act_2', 'target': 'cg_1',340                                                 'id': '3368add44347310eaef1f26f25909026'},341            '05f91b45a15b37d7b0c96d3ff94bff80': {'is_default': False, 'source': 'cg_1', 'target': 'end_event_id',342                                                 'id': '05f91b45a15b37d7b0c96d3ff94bff80'},343            '3fc89273786a36b8a6e7beac8301274d': {'is_default': False, 'source': 'pg_1', 'target': 'act_1',344                                                 'id': '3fc89273786a36b8a6e7beac8301274d'},345            '76caeed0e6053fea9db84a89f56a74a8': {'is_default': False, 'source': 'pg_1', 'target': 'act_2',346                                                 'id': '76caeed0e6053fea9db84a89f56a74a8'},347            '76casdgd0e6053ea9db84a89f56a1234': {'is_default': False, 'source': 'pg_1', 'target': 'cg_1',348                                                 'id': '76caeed0e6053fea9db84a89f56a74a8'}},349        'gateways': {350            'cg_1': {'type': 'ConvergeGateway', 'outgoing': '05f91b45a15b37d7b0c96d3ff94bff80',351                     'incoming': ['82b12b6aae533e55bdcc5bccfb014c2d',352                                  '3368add44347310eaef1f26f25909026',353                                  '76casdgd0e6053ea9db84a89f56a1234'], 'id': 'cg_1',354                     'name': None},355            'pg_1': {'outgoing': ['3fc89273786a36b8a6e7beac8301274d',356                                  '76caeed0e6053fea9db84a89f56a74a8',357                                  '76casdgd0e6053ea9db84a89f56a1234'],358                     'incoming': ['27a9cdeaef623d37834ac6917d05eac5'], 'name': None, 'converge_gateway_id': 'cg_1',359                     'type': 'ParallelGateway', 'id': 'pg_1'}},360        'start_event': {'type': 'EmptyStartEvent', 'outgoing': '27a9cdeaef623d37834ac6917d05eac5', 'incoming': '',361                        'id': 'start_event_id', 'name': None}, 'data': {'inputs': {}, 'outputs': {}},362        'id': 'c986802cd1e23a5f920c85b005f16dc3'}363def flow_invalid_case_1():364    start = EmptyStartEvent(id=start_event_id)365    act_1 = ServiceActivity(id=act_id(1))366    pg = ParallelGateway(id=parallel_gw_id(1))367    act_2 = ServiceActivity(id=act_id(2))368    act_3 = ServiceActivity(id=act_id(3))369    eg = ExclusiveGateway(id=exclusive_gw_id(1), conditions={370        0: '123',371        1: '456'372    })373    act_4 = ServiceActivity(id=act_id(4))374    cg = ConvergeGateway(id=converge_gw_id(1))375    end = EmptyEndEvent(id=end_event_id)376    start.extend(act_1).extend(pg).connect(377        act_2,378        act_3,379        eg380    ).to(eg).connect(381        act_3,382        act_4383    )384    act_2.connect(cg)385    act_3.connect(cg)386    act_4.connect(cg)387    cg.extend(end)388    return build_tree(start)389def flow_invalid_case_2():390    start = EmptyStartEvent(id=start_event_id)391    act_1 = ServiceActivity(id=act_id(1))392    eg = ExclusiveGateway(id=exclusive_gw_id(1), conditions={393        0: '123',394        1: '456'395    })396    act_2 = ServiceActivity(id=act_id(2))397    pg = ParallelGateway(id=parallel_gw_id(1))398    act_3 = ServiceActivity(id=act_id(3))399    act_4 = ServiceActivity(id=act_id(4))400    cg = ConvergeGateway(id=converge_gw_id(1))401    end = EmptyEndEvent(id=end_event_id)402    start.extend(act_1).extend(eg).connect(403        act_3,404        act_2405    ).to(act_2).extend(pg).connect(406        act_3,407        act_4408    ).converge(cg).extend(end)409    return build_tree(start)410flow_valid_edge_cases = [411    {412        'case': flow_valid_edge_case_1,413    },414    {415        'case': flow_valid_edge_case_2,416    }417]418flow_invalid_cases = [419    {420        'case': flow_invalid_case_1,421        'assert_invalid': act_id(3)422    },...

package.py

Source:package.py

1# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other2# Spack Project Developers. See the top-level COPYRIGHT file for details.3#4# SPDX-License-Identifier: (Apache-2.0 OR MIT)5import glob6import os7from spack import *8class Converge(Package):9    """CONVERGE is a revolutionary computational fluid dynamics (CFD) program10    that eliminates the grid generation bottleneck from the simulation process.11    CONVERGE was developed by engine simulation experts and is straightforward12    to use for both engine and non-engine simulations. Unlike many CFD13    programs, CONVERGE automatically generates a perfectly orthogonal,14    structured grid at runtime based on simple, user-defined grid control15    parameters. This grid generation method completely eliminates the need to16    manually generate a grid. In addition, CONVERGE offers many other features17    to expedite the setup process and to ensure that your simulations are as18    computationally efficient as possible."""19    homepage = "https://www.convergecfd.com/"20    url      = "https://download.convergecfd.com/download/CONVERGE_2.4/Full_Solver_Packages/converge_install_2.4.10.tar.gz"21    # In order to view available versions, you need to register for an account:22    # https://download.convergecfd.com/wp-login.php?action=register23    version('2.4.10', sha256='5d3c39894598d2395149cfcc653af13b8b1091177290edd62fcf22c7e830d410')24    version('2.3.23', sha256='1217d16eaf9d263f917ee468778508bad9dacb7e4397a293cfa6467f39fb4c52')25    version('2.2.0',  sha256='3885acbaf352c718ea69f0206c858a01be02f0928ffee738e4aceb1dd939a77a',26            url="https://download.convergecfd.com/download/CONVERGE_2.2/Full_Solver_Packages/converge_install_2.2.0_042916.tar.gz")27    version('2.1.0',  sha256='6b8896d42cf7b9013cae5456f4dc118306a5bd271d4a15945ceb7dae913e825a',28            url="https://download.convergecfd.com/download/CONVERGE_2.1/Full_Solver_Packages/converge_install_2.1.0_111615.tar.gz")29    version('2.0.0',  sha256='f32c4824eb33724d85e283481d67ebd0630b1406011c528d775028bb2546f34e',30            url="https://download.convergecfd.com/download/CONVERGE_2.0/Full_Solver_Packages/converge_install_2.0.0_090214.tar.gz")31    variant('mpi', default=True, description='Build with MPI support')32    # The following MPI libraries are compatible with CONVERGE:33    #34    # +--------------+---------+---------+---------+---------+---------+35    # | MPI Packages |  v2.0   |  v2.1   |  v2.2   |  v2.3   |  v2.4   |36    # +--------------+---------+---------+---------+---------+---------+37    # | HP-MPI       | 2.0.3+  | 2.0.3+  | 2.0.3+  | 2.0.3+  |         |38    # | Intel MPI    |         |         |         |         | 17.0.98 |39    # | MPICH        | ?.?.?   | ?.?.?   | 1.2.1   | 3.1.4   | ?.?.?   |40    # | MVAPICH2     | ?.?.?   |         |         |         |         |41    # | Open MPI     | 1.0-1.4 | 1.0-1.4 | 1.5-1.8 | 1.5-1.8 | 1.10    |42    # | Platform MPI |         |         | 9.1.2   | 9.1.2   | 9.1.2   |43    # +--------------+---------+---------+---------+---------+---------+44    #45    # NOTE: HP-MPI was bought out by Platform MPI46    #47    # These version requirements are more strict than for most packages.48    # Since the tarball comes with pre-compiled executables,49    # the version of libmpi.so must match exactly, or else50    # you will end up with missing libraries and symbols.51    depends_on('mpi', when='+mpi')52    # FIXME: Concretization is currently broken, so this causes:53    #     $ spack spec converge54    # to crash. You must explicitly state what MPI version you want:55    #     $ spack spec converge@2.4.10 +mpi ^openmpi@:1.1056    #57    # TODO: Add version ranges for other MPI libraries58    depends_on('openmpi@1.10.0:1.10.999', when='@2.4.0:2.4.999+mpi^openmpi')59    depends_on('openmpi@1.5:1.8',         when='@2.2:2.3+mpi^openmpi')60    depends_on('openmpi@:1.4',            when='@:2.1+mpi^openmpi')61    # TODO: Add packages for hp-mpi and platform-mpi62    # conflicts('^hp-mpi', when='@2.4:')63    conflicts('^intel-mpi', when='@:2.3')64    conflicts('^intel-parallel-studio+mpi', when='@:2.3')65    # conflicts('^platform-mpi', when='@:2.1')66    conflicts('^spectrum-mpi')67    # Licensing68    license_required = True69    license_comment = '#'70    license_files = ['license/license.lic']71    license_vars = ['RLM_LICENSE']72    license_url = 'http://www.reprisesoftware.com/RLM_License_Administration.pdf'73    def url_for_version(self, version):74        url = "https://download.convergecfd.com/download/CONVERGE_{0}/Full_Solver_Packages/converge_install_{1}.tar.gz"75        return url.format(version.up_to(2), version)76    def install(self, spec, prefix):77        # 2.0.078        # converge                      -> converge-2.0.0-hpmpi-09021479        # converge-2.0.0-hpmpi-090214   -> libmpi.so.1, libmpio.so.180        # converge-2.0.0-mpich2-090214  -> libmpich.so.1.281        # converge-2.0.0-mvapich-090214 -> libibumad.so.182        # converge-2.0.0-openmpi-090214 -> libmpi.so.083        # converge-2.0.0-serial-09021484        # make_surface85        # post_convert86        # 2.1.087        # converge                      -> converge-2.1.0-hpmpi-11161588        # converge-2.1.0-hpmpi-111615   -> libmpi.so.1, libmpio.so.189        # converge-2.1.0-mpich2-111615  -> libmpich.so.1.290        # converge-2.1.0-openmpi-111615 -> libmpi.so.091        # converge-2.1.0-serial-11161592        # make_surface93        # post_convert94        # 2.2.095        # converge                      -> converge-2.2.0-hpmpi-04291696        # converge-2.2.0-hpmpi-042916   -> libmpi.so.1, libmpio.so.197        # converge-2.2.0-mpich2-04291698        # converge-2.2.0-openmpi-042916 -> libmpi.so.199        # converge-2.2.0-pmpi-042916    -> libmpi.so.1, libmpio.so.1100        # converge-2.2.0-serial-042916101        # make_surface102        # post_convert103        # 2.3.23104        # converge-2.3.23-hpmpi-linux-64    -> libmpi.so.1, libmpio.so.1105        # converge-2.3.23-mpich2-linux-64   -> libmpi.so.12106        # converge-2.3.23-openmpi-linux-64  -> libmpi.so.1107        # converge-2.3.23-pmpi-linux-64     -> libmpi.so.1, libmpio.so.1108        # converge-2.3.23-serial-linux-64109        # make_surface_64110        # post_convert_mpich_64             -> libmpi.so.12111        # post_convert_ompi_64              -> libmpi.so.1112        # post_convert_pmpi_64              -> libmpi.so.1, libmpio.so.1113        # post_convert_serial_64114        # 2.4.10115        # converge-2.4.10-intel     -> libmpi.so.12, libmpifort.so.12116        # converge-2.4.10-mpich     -> libmpi.so.12117        # converge-2.4.10-ompi      -> libmpi.so.12118        # converge-2.4.10-pmpi      -> libmpi.so.1, libmpio.so.1119        # converge-2.4.10-serial120        # make_surface_64121        # post_convert_mpich_64     -> libmpi.so.12122        # post_convert_ompi_64      -> libmpi.so.1123        # post_convert_pmpi_64      -> libmpi.so.1124        # post_convert_serial_64125        # The CONVERGE tarball comes with binaries for several MPI libraries.126        # Only install the binary that matches the MPI we are building with.127        with working_dir('l_x86_64/bin'):128            if '~mpi' in spec:129                converge = glob.glob('converge-*-serial*')130                post_convert = glob.glob('post_convert_serial*')131            elif 'hp-mpi' in spec:132                converge = glob.glob('converge-*-hpmpi*')133                # No HP-MPI version of post_convert134                post_convert = glob.glob('post_convert_serial*')135            elif 'intel-mpi' in spec or 'intel-parallel-studio+mpi' in spec:136                converge = glob.glob('converge-*-intel*')137                # No Intel MPI version of post_convert138                post_convert = glob.glob('post_convert_serial*')139            elif 'mpich' in spec:140                converge = glob.glob('converge-*-mpich*')141                post_convert = glob.glob('post_convert_mpich*')142            elif 'mvapich2' in spec:143                converge = glob.glob('converge-*-mvapich*')144                # MVAPICH2 hasn't been supported since CONVERGE145                # came with a single serial post_convert146                post_convert = glob.glob('post_convert')147            elif 'openmpi' in spec:148                converge = glob.glob('converge-*-o*mpi*')149                post_convert = glob.glob('post_convert_o*mpi*')150            elif 'platform-mpi' in spec:151                converge = glob.glob('converge-*-pmpi*')152                post_convert = glob.glob('post_convert_pmpi*')153            else:154                raise InstallError('Unsupported MPI provider')155            make_surface = glob.glob('make_surface*')156            # Old versions of CONVERGE come with a single serial post_convert157            if not post_convert:158                post_convert = glob.glob('post_convert')159            # Make sure glob actually found something160            if not converge:161                raise InstallError('converge executable not found')162            if not post_convert:163                raise InstallError('post_convert executable not found')164            if not make_surface:165                raise InstallError('make_surface executable not found')166            # Make sure glob didn't find multiple matches167            if len(converge) > 1:168                raise InstallError('multiple converge executables found')169            if len(post_convert) > 1:170                raise InstallError('multiple post_convert executables found')171            if len(make_surface) > 1:172                raise InstallError('multiple make_surface executables found')173            converge = converge[0]174            post_convert = post_convert[0]175            make_surface = make_surface[0]176            mkdir(prefix.bin)177            # Install the executables178            install(converge,     join_path(prefix.bin, converge))179            install(post_convert, join_path(prefix.bin, post_convert))180            install(make_surface, join_path(prefix.bin, make_surface))181        with working_dir(prefix.bin):182            # Create generic symlinks to all executables183            if not os.path.exists('converge'):184                os.symlink(converge, 'converge')185            if not os.path.exists('post_convert'):186                os.symlink(post_convert, 'post_convert')187            if not os.path.exists('make_surface'):188                os.symlink(make_surface, 'make_surface')189    def setup_run_environment(self, env):190        # CONVERGE searches for a valid license file in:191        #     $CONVERGE_ROOT/license/license.lic...

TestSimulator.py

Source:TestSimulator.py

1#!/usr/bin/env python2# encoding: utf-83"""4TestSimulator.py5Created by Fredrick Stakem on 2010-05-20.6Copyright (c) 2010 __Research__. All rights reserved.7"""8# Import libraries9#------------------------------------------------------------------------------10import Simulator as s11import pdb12import numpy13import scipy14import scipy.signal15import pylab16import time17import math18from enum import Enum19from Globals import *20# Filesystem paramters21#------------------------------------------------------------------------------22dataRoot = "/Users/fstakem/Data/Movements_5_1_08/"23root = "/Users/fstakem/Research/PhD/2010_Research/SeperateConvergence/code/"24libDir = root + "lib/"25logDir = root + "log/"26outputDir = root + "output/"27# Simulation data28#------------------------------------------------------------------------------29movement = "Stacking"30simulation = 131inputFile = dataRoot + movement + "/Simulation" + str(simulation) + \32			"/positionLog.txt"33# Transmission parameters34#------------------------------------------------------------------------------35predictionInterval = 10036samplingInterval = 1037heartbeat = 50038drThreshold = 0.02539convergenceType = InterpolationType.Time40# Network parameters41#------------------------------------------------------------------------------42delay = 10043jitter = 4044packetLoss = 045# Reconstruction parameters46#------------------------------------------------------------------------------47convergenceTime = 5048longConvergenceTime = 10049# Calculation parameters50#------------------------------------------------------------------------------51jumpThreshold = 052jumpSpacing = 153# Simulate the transmission and reconstruction algorithms54#------------------------------------------------------------------------------55startTimeTotal = time.time()56transmittedData = []57simNumber = inputFile.split('/')[-2][-1]58data = s.transmitData(inputFile, logDir, predictionInterval,59					  samplingInterval, heartbeat, drThreshold,60					  delay, jitter, packetLoss)61snapData = s.snapReconstructData(data[5], 62								 logDir, 63								 simNumber, 64								 samplingInterval)[0]								65convergeData = s.convergeData(data[5], logDir, simNumber, samplingInterval,66			   				  convergenceTime)[0]								67varConvergeData = s.varConvergeData(data[5], logDir, simNumber, samplingInterval,68								    convergenceTime, longConvergenceTime)[0]69data.append(snapData)70data.append(convergeData)71data.append(varConvergeData)72print "Total time spent simulating the transmission: " + str(time.time() - \73															 startTimeTotal)74print75# Set the variables for the data76#------------------------------------------------------------------------------77initialData = data[1]78snapData = data[6]79convergeData = data[7]80varConvergeData = data[8]81# Calculate the results and statistics82#------------------------------------------------------------------------------83inputJump = s.calculateStats( s.findDistanceBetweenSamples(initialData,84										 				   jumpThreshold,85										 				   jumpSpacing) )										86snapError = s.calculateStats( s.findDistanceError(initialData,87								    			  snapData) )88snapJump = s.calculateStats( s.findDistanceBetweenSamples(snapData,89									 				   	  jumpThreshold,90									 				   	  jumpSpacing) )91convergeError = s.calculateStats( s.findDistanceError(initialData,92													  convergeData) )93convergeJump = s.calculateStats( s.findDistanceBetweenSamples(convergeData,94															  jumpThreshold,95															  jumpSpacing) )96varConvergeError = s.calculateStats( s.findDistanceError(initialData,97														 varConvergeData) )98varConvergeJump = s.calculateStats( s.findDistanceBetweenSamples(varConvergeData,99																 jumpThreshold,100																 jumpSpacing) )101																102# Output the statistics103#------------------------------------------------------------------------------104print "Jump:"105print "\tInput:\t\t" + str(inputJump)106print "\tSnap:\t\t" + str(snapJump)107print "\tConverge:\t" + str(convergeJump) 108print "\tVar Converge:\t" + str(varConvergeJump)109print "Error:"110print "\tSnap:\t\t" + str(snapError) 111print "\tConverge:\t" + str(convergeError)112print "\tVar Converge:\t" + str(varConvergeError)113# Seperate the singals for plotting114#------------------------------------------------------------------------------115initialTime, initialX, initialY, initialZ = s.splitData(initialData)116snapTime, snapX, snapY, snapZ = s.splitData(snapData)117convergeTime, convergeX, convergeY, convergeZ = s.splitData(convergeData)118varConvergeTime, varConvergeX, varConvergeY, varConvergeZ = s.splitData(varConvergeData)119lowerBound = 19000120upperBound = 25000121initialTime, initialX = s.cropData(initialTime, initialX, lowerBound, upperBound)122snapTime, snapX = s.cropData(snapTime, snapX, lowerBound, upperBound)123convergeTime, convergeX = s.cropData(convergeTime, convergeX, lowerBound, upperBound)124varConvergeTime, varConvergeX = s.cropData(varConvergeTime, varConvergeX, lowerBound, upperBound)125																	126# Plot the signals127#------------------------------------------------------------------------------128figure = 1129pylab.figure(figure)130pylab.plot(initialTime, initialX, 'k-')131pylab.plot(snapTime, snapX, 'b-')132pylab.plot(convergeTime, convergeX, 'r-')133pylab.plot(varConvergeTime, varConvergeX, 'g-')134figure = 2135pylab.figure(figure)136pylab.plot(varConvergeTime, varConvergeX, 'g-')...

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