testKinetics.cpp File Reference

#include "header.h"
#include "../shell/Shell.h"
#include "ReadKkit.h"
#include "ReadCspace.h"
#include "EnzBase.h"
#include "MMenz.h"
#include "ReacBase.h"
#include "Reac.h"

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Functions
double	estT (double s)
bool	isClose (double x, double y, double tol)
void	testKinetics ()
void	testKineticsProcess ()
void	testMMenz ()
void	testMMenzProcess ()
void	testMpiKinetics ()
void	testPoolVolumeScaling ()
void	testReacVolumeScaling ()
void	testReadCspace ()
void	testReadKkit ()
void	testTwoReacGetNeighbors ()
void	testVolSort ()
void	testWriteKkit (Id id)

Function Documentation

double estT

(

double

s

)

Definition at line 223 of file testKinetics.cpp.

References moose::log(), and s0.

Referenced by testMMenzProcess().

{
    double E = 1.0;
    double Km = 1.0;
    double kcat = 1.0;
    double s0 = 1.0;
    double c = -Km * log( s0 ) - s0;
    double t = (-1.0 /( E * kcat ) ) * ( ( Km * log( s ) + s ) + c );
    return t;
}

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bool isClose	(	double	x,
		double	y,
		double	tol
	)

Definition at line 35 of file testKinetics.cpp.

{
    return ( fabs( x - y ) < tol * 1e-8 );
}

void testKinetics

(

)

Definition at line 331 of file testKinetics.cpp.

References testMMenz(), testPoolVolumeScaling(), testReacVolumeScaling(), testReadCspace(), testTwoReacGetNeighbors(), and testVolSort().

{
    testTwoReacGetNeighbors();
    testMMenz();
    testPoolVolumeScaling();
    testReacVolumeScaling();
    testReadCspace();
    testVolSort();

    // This is now handled with real models in the regression tests.
    // testWriteKkit( Id() );
}

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void testKineticsProcess

(

)

Definition at line 348 of file testKinetics.cpp.

References testMMenzProcess().

{
    testMMenzProcess();
}

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void testMMenz

(

)

Definition at line 198 of file testKinetics.cpp.

References Eref::data(), Shell::doCreate(), Shell::doDelete(), doubleEq(), Id::eref(), MMenz::vEnz(), MMenz::vGetKcat(), MMenz::vGetKm(), MMenz::vProcess(), MMenz::vReinit(), MMenz::vSetKcat(), MMenz::vSetKm(), and MMenz::vSub().

Referenced by testKinetics().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id mmid = shell->doCreate( "MMenz", Id(), "mm", 1 ); // mmenz
    MMenz m;
    ProcInfo p;

    m.vSetKm( mmid.eref(), 5.0 );
    m.vSetKcat( mmid.eref(), 4.0 );
    m.vReinit( mmid.eref(), &p );
    m.vSub( 2 );
    m.vEnz( 3 );
    assert( doubleEq( m.vGetKm( mmid.eref() ), 5.0 ) );
    assert( doubleEq( m.vGetKcat( mmid.eref() ), 4.0 ) );
    m.vProcess( mmid.eref(), &p );

    shell->doDelete( mmid );
    cout << "." << flush;
}

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void testMMenzProcess

(

)

Definition at line 234 of file testKinetics.cpp.

References Eref::data(), Shell::doAddMsg(), Shell::doCreate(), Shell::doDelete(), Shell::doReinit(), Shell::doSetClock(), Shell::doStart(), doubleApprox(), Shell::doUseClock(), Id::eref(), estT(), and Field< A >::set().

Referenced by testKineticsProcess().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    // This set is the test kinetic calculation using MathFunc
    Id nid = shell->doCreate( "Neutral", Id(), "n", 1 );
    // This set is the reference kinetic calculation using MMEnz
    Id pid = shell->doCreate( "Pool", nid, "p", 1 ); // substrate
    Id qid = shell->doCreate( "Pool", nid, "q", 1 );    // enz mol
    Id rid = shell->doCreate( "Pool", nid, "r", 1 ); // product
    Id mmid = shell->doCreate( "MMenz", nid, "mm", 1 ); // mmenz

    Id tabid2 = shell->doCreate( "Table", nid, "tab2", 1 ); //output plot

    Field< double >::set( mmid, "Km", 1.0 );
    Field< double >::set( mmid, "kcat", 1.0 );
    Field< double >::set( pid, "nInit", 1.0 );
    Field< double >::set( qid, "nInit", 1.0 );
    Field< double >::set( rid, "nInit", 0.0 );

    shell->doAddMsg( "Single", ObjId( mmid ), "sub", ObjId( pid ), "reac" );
    shell->doAddMsg( "Single", ObjId( mmid ), "prd", ObjId( rid ), "reac" );
    shell->doAddMsg( "Single", ObjId( qid ), "nOut", ObjId( mmid ), "enzDest" );
    shell->doAddMsg( "Single", ObjId( pid ), "nOut", ObjId( tabid2 ), "input" );
    shell->doSetClock( 0, 0.01 );
    shell->doSetClock( 1, 0.01 );
    shell->doUseClock( "/n/mm,/n/tab2", "process", 0 );
    shell->doUseClock( "/n/#[ISA=Pool]", "process", 1 );

    // Now run models and compare outputs

    shell->doReinit();
    shell->doStart( 10 );

    vector< double > vec = Field< vector< double > >::get( tabid2, "vec" );
    assert( vec.size() == 1001 );
    for ( unsigned int i = 0; i < vec.size(); ++i ) {
        double t = 0.01 * i;
        double et = estT( vec[i] );
        assert( doubleApprox( t, et ) );
    }

    shell->doDelete( nid );
    cout << "." << flush;
}

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void testMpiKinetics

(

)

Definition at line 344 of file testKinetics.cpp.

{
}

void testPoolVolumeScaling

(

)

Definition at line 40 of file testKinetics.cpp.

References Eref::data(), Shell::doAddMsg(), Shell::doCreate(), Shell::doDelete(), doubleEq(), Id::eref(), Field< A >::get(), NA, PI, Field< A >::set(), and Id::value().

Referenced by testKinetics().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id comptId = shell->doCreate( "CylMesh", Id(), "cyl", 1 );
    Id meshId( comptId.value() + 1 );
    Id poolId = shell->doCreate( "Pool", comptId, "pool", 1 );

    ObjId mid = shell->doAddMsg( "OneToOne",
        ObjId( poolId, 0 ), "requestVolume",
        ObjId( meshId, 0 ), "get_volume" );

    assert( mid != ObjId() );

    vector< double > coords( 9, 0.0 );
    double x1 = 100e-6;
    double r0 = 10e-6;
    double r1 = 5e-6;
    double lambda = x1;
    coords[3] = x1;
    coords[6] = r0;
    coords[7] = r1;
    coords[8] = lambda;

    Field< vector< double > >::set( comptId, "coords", coords );

    double volume = Field< double >::get( poolId, "volume" );
    assert( doubleEq( volume, PI * x1 * (r0+r1) * (r0+r1) / 4.0 ) );

    Field< double >::set( poolId, "n", 400 );
    double volscale = 1 / ( NA * volume );
    double conc = Field< double >::get( poolId, "conc" );
    assert( doubleEq( conc, 400 * volscale ) );
    Field< double >::set( poolId, "conc", 500 * volscale );
    double n = Field< double >::get( poolId, "n" );
    assert( doubleEq( n, 500 ) );

    Field< double >::set( poolId, "nInit", 650 );
    double concInit = Field< double >::get( poolId, "concInit" );
    assert( doubleEq( concInit, 650 * volscale ) );
    Field< double >::set( poolId, "concInit", 10 * volscale );
    n = Field< double >::get( poolId, "nInit" );
    assert( doubleEq( n, 10 ) );

    shell->doDelete( comptId );
    cout << "." << flush;
}

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void testReacVolumeScaling

(

)

Definition at line 87 of file testKinetics.cpp.

References Eref::data(), Shell::doAddMsg(), Shell::doCreate(), Shell::doDelete(), doubleEq(), Id::eref(), Field< A >::get(), NA, Field< A >::set(), and Id::value().

Referenced by testKinetics().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id comptId = shell->doCreate( "CubeMesh", Id(), "cube", 1 );
    Id meshId( comptId.value() + 1 );
    Id subId = shell->doCreate( "Pool", comptId, "sub", 1 );
    Id prdId = shell->doCreate( "Pool", comptId, "prd", 1 );
    Id reacId = shell->doCreate( "Reac", comptId, "reac", 1 );

    double vol1 = 1e-15;

    ObjId mid = shell->doAddMsg( "OneToOne",
        subId, "requestVolume", meshId, "get_volume" );
    assert( mid != ObjId() );
    mid = shell->doAddMsg( "OneToOne",
        prdId, "requestVolume", meshId, "get_volume" );
    assert( mid != ObjId() );

    vector< double > coords( 9, 10.0e-6 );
    coords[0] = coords[1] = coords[2] = 0;

    Field< vector< double > >::set( comptId, "coords", coords );

    double volume = Field< double >::get( comptId, "volume" );
    assert( doubleEq( volume, vol1 ) );

    ObjId ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
    assert( ret != ObjId() );
    ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
    assert( ret != ObjId() );

    Field< double >::set( reacId, "Kf", 2 );
    Field< double >::set( reacId, "Kb", 3 );
    double x = Field< double >::get( reacId, "kf" );
    assert( doubleEq( x, 2 ) );
    x = Field< double >::get( reacId, "kb" );
    assert( doubleEq( x, 3 ) );

    ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
    assert( ret != ObjId() );
    double conv = 1.0 / ( NA * vol1 );
    x = Field< double >::get( reacId, "kf" );
    assert( doubleEq( x, 2 * conv ) );
    x = Field< double >::get( reacId, "kb" );
    assert( doubleEq( x, 3 ) );

    ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
    assert( ret != ObjId() );
    ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
    assert( ret != ObjId() );
    x = Field< double >::get( reacId, "kf" );
    assert( doubleEq( x, 2 * conv * conv ) );
    x = Field< double >::get( reacId, "kb" );
    assert( doubleEq( x, 3 * conv ) );

    shell->doDelete( comptId );
    cout << "." << flush;
}

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void testReadCspace

(

)

Definition at line 191 of file testKinetics.cpp.

References ReadCspace::testReadModel().

Referenced by testKinetics().

{
    ReadCspace rc;
    rc.testReadModel();
    cout << "." << flush;
}

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void testReadKkit

(

)

Definition at line 19 of file testKinetics.cpp.

References Eref::data(), Shell::doDelete(), ReadKkit::dumpPlots(), Id::eref(), ReadKkit::read(), and ReadKkit::run().

{
    ReadKkit rk;
    // rk.read( "test.g", "dend", 0 );
    Id base = rk.read( "foo.g", "dend", Id() );
    assert( base != Id() );
    // Id kinetics = s->doFind( "/kinetics" );

    Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
    rk.run();
    rk.dumpPlots( "dend.plot" );

    s->doDelete( base );
    cout << "." << flush;
}

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void testTwoReacGetNeighbors

(

)

Definition at line 147 of file testKinetics.cpp.

References Eref::data(), Shell::doAddMsg(), Shell::doCreate(), Shell::doDelete(), Id::element(), Id::eref(), Element::getNeighbors(), Reac::initCinfo(), and Id::value().

Referenced by testKinetics().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id comptId = shell->doCreate( "CubeMesh", Id(), "cube", 1 );
    Id meshId( comptId.value() + 1 );
    Id subId = shell->doCreate( "Pool", comptId, "sub", 1 );
    Id prdId = shell->doCreate( "Pool", comptId, "prd", 1 );
    Id reacId = shell->doCreate( "Reac", comptId, "reac", 1 );

    ObjId mid = shell->doAddMsg( "OneToOne",
        subId, "requestVolume", meshId, "get_volume" );
    assert( mid != ObjId() );
    mid = shell->doAddMsg( "OneToOne",
        prdId, "requestVolume", meshId, "get_volume" );
    assert( mid != ObjId() );

    ObjId ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
    assert( ret != ObjId() );
    ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
    assert( ret != ObjId() );

    ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
    assert( ret != ObjId() );

    vector< Id > pools;
    unsigned int num = reacId.element()->getNeighbors( pools,
        Reac::initCinfo()->findFinfo( "toSub" ) );
    assert( num == 2 );
    assert( pools[0] == subId );
    assert( pools[1] == subId );

    pools.clear();
    num = reacId.element()->getNeighbors( pools,
        Reac::initCinfo()->findFinfo( "sub" ) );
    assert( num == 2 );
    assert( pools[0] == subId );
    assert( pools[1] == subId );

    shell->doDelete( comptId );
    cout << "." << flush;
}

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void testVolSort

(

)

Definition at line 292 of file testKinetics.cpp.

References findVolOrder().

Referenced by testKinetics().

{
    vector< unsigned int > findVolOrder( const vector< double >& vols );
    vector< double > vols( 8 );
    vols[0] = 7;
    vols[1] = 8;
    vols[2] = 6;
    vols[3] = 5;
    vols[4] = 1;
    vols[5] = 2;
    vols[6] = 3;
    vols[7] = 4;
    vector< unsigned int > order = findVolOrder( vols );
    // The order is the rank of the volume entry, largest should be 0.
    assert( order[0] == 1 );
    assert( order[1] == 0 );
    assert( order[2] == 2 );
    assert( order[3] == 3 );
    assert( order[4] == 7 );
    assert( order[5] == 6 );
    assert( order[6] == 5 );
    assert( order[7] == 4 );

    // This is a sequence which failed in a model test, despite the
    // above test working.
    vols.resize(5);
    vols[0] = 1e-15;
    vols[1] = 3e-15;
    vols[2] = -1;
    vols[3] = 2e-15;
    vols[4] = 5e-15;
    order = findVolOrder( vols );
    assert( order[0] == 4 );
    assert( order[1] == 1 );
    assert( order[2] == 3 );
    assert( order[3] == 0 );
    assert( order[4] == 2 );
}

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void testWriteKkit

(

Id

id

)

Definition at line 285 of file testKinetics.cpp.

References writeKkit().

{
    extern void writeKkit( Id model, const string& s );
    writeKkit( id, "kkitWriteTest.g" );
    cout << "." << flush;
}

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