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apply uncrustify (#20)
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10 files changed

+131
-129
lines changed

10 files changed

+131
-129
lines changed

‎src/common/pmpl.hpp‎

Lines changed: 18 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -22,17 +22,17 @@ namespace hpcReact
2222
{
2323
#if defined(HPCREACT_USE_DEVICE)
2424
#if defined(HPCREACT_USE_CUDA)
25-
#define deviceMalloc( PTR, BYTES ) cudaMalloc( PTR, BYTES );
26-
#define deviceMallocManaged( PTR, BYTES ) cudaMallocManaged( PTR, BYTES );
27-
#define deviceDeviceSynchronize() cudaDeviceSynchronize();
28-
#define deviceMemCpy( DST, SRC, BYTES, KIND ) cudaMemcpy( DST, SRC, BYTES, KIND );
29-
#define deviceFree( PTR ) cudaFree( PTR );
25+
#define deviceMalloc( PTR, BYTES ) cudaMalloc( PTR, BYTES );
26+
#define deviceMallocManaged( PTR, BYTES ) cudaMallocManaged( PTR, BYTES );
27+
#define deviceDeviceSynchronize() cudaDeviceSynchronize();
28+
#define deviceMemCpy( DST, SRC, BYTES, KIND ) cudaMemcpy( DST, SRC, BYTES, KIND );
29+
#define deviceFree( PTR ) cudaFree( PTR );
3030
#elif defined(HPCREACT_USE_HIP)
31-
#define deviceMalloc( PTR, BYTES ) hipMalloc( PTR, BYTES );
32-
#define deviceMallocManaged( PTR, BYTES ) hipMallocManaged( PTR, BYTES );
33-
#define deviceDeviceSynchronize() hipDeviceSynchronize();
34-
#define deviceMemCpy( DST, SRC, BYTES, KIND ) hipMemcpy( DST, SRC, BYTES, KIND );
35-
#define deviceFree( PTR ) hipFree( PTR );
31+
#define deviceMalloc( PTR, BYTES ) hipMalloc( PTR, BYTES );
32+
#define deviceMallocManaged( PTR, BYTES ) hipMallocManaged( PTR, BYTES );
33+
#define deviceDeviceSynchronize() hipDeviceSynchronize();
34+
#define deviceMemCpy( DST, SRC, BYTES, KIND ) hipMemcpy( DST, SRC, BYTES, KIND );
35+
#define deviceFree( PTR ) hipFree( PTR );
3636
#endif
3737
#endif
3838

@@ -130,12 +130,18 @@ void genericKernelWrapper( int const N, DATA_TYPE * const hostData, LAMBDA && fu
130130
genericKernel <<< 1, 1 >>> ( std::forward< LAMBDA >( func ), deviceData );
131131

132132
cudaError_t e = cudaGetLastError();
133-
if (e != cudaSuccess) { fprintf(stderr, "launch error: %s\n", cudaGetErrorString(e)); abort(); }
133+
if( e != cudaSuccess )
134+
{
135+
fprintf( stderr, "launch error: %s\n", cudaGetErrorString( e )); abort();
136+
}
134137

135138
deviceDeviceSynchronize();
136139

137140
e = cudaGetLastError();
138-
if (e != cudaSuccess) { fprintf(stderr, "post-sync error: %s\n", cudaGetErrorString(e)); abort(); }
141+
if( e != cudaSuccess )
142+
{
143+
fprintf( stderr, "post-sync error: %s\n", cudaGetErrorString( e )); abort();
144+
}
139145

140146
deviceMemCpy( hostData, deviceData, N * sizeof(DATA_TYPE), cudaMemcpyDeviceToHost );
141147
deviceFree( deviceData );

‎src/reactions/exampleSystems/unitTests/testMomasEasyCase.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,7 @@ void testMoMasAllEquilibriumHelper()
6565
targetAggregatePrimarySpeciesConcentration,
6666
logInitialPrimarySpeciesConcentration,
6767
logPrimarySpeciesConcentrationCopy );
68-
});
68+
} );
6969

7070
double const expectedPrimarySpeciesConcentrations[numPrimarySpecies] =
7171
{

‎src/reactions/exampleSystems/unitTests/testMomasMediumCase.cpp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -60,13 +60,13 @@ void testMoMasMediumEquilibriumHelper()
6060
log( initialPrimarySpeciesConcentration[3] ),
6161
log( initialPrimarySpeciesConcentration[4] )
6262
};
63-
63+
6464
EquilibriumReactionsType::enforceEquilibrium_Aggregate( 0,
6565
hpcReact::MoMasBenchmark::mediumCaseParams.equilibriumReactionsParameters(),
6666
targetAggregatePrimarySpeciesConcentration,
6767
logInitialPrimarySpeciesConcentration,
6868
logPrimarySpeciesConcentrationCopy );
69-
});
69+
} );
7070

7171
double const expectedPrimarySpeciesConcentrations[numPrimarySpecies] =
7272
{

‎src/reactions/massActions/MassActions.hpp‎

Lines changed: 4 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ void calculateLogSecondarySpeciesConcentration( PARAMS_DATA const & params,
8282
INDEX_TYPE >( params,
8383
logPrimarySpeciesConcentrations,
8484
logSecondarySpeciesConcentrations,
85-
[](INDEX_TYPE, INDEX_TYPE, REAL_TYPE ){} );
85+
[]( INDEX_TYPE, INDEX_TYPE, REAL_TYPE ){} );
8686
}
8787

8888

@@ -154,8 +154,7 @@ void calculateAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA const & params,
154154
for( int k=0; k<numPrimarySpecies; ++k )
155155
{
156156
REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
157-
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
158-
i+numSecondarySpecies ) *
157+
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j, i+numSecondarySpecies ) *
159158
dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;
160159
}
161160
}
@@ -248,12 +247,10 @@ void calculateTotalAndMobileAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA c
248247
for( int k=0; k<numPrimarySpecies; ++k )
249248
{
250249
REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
251-
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
252-
i+numSecondarySpecies ) *
250+
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j, i+numSecondarySpecies ) *
253251
dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;
254252

255-
dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
256-
i+numSecondarySpecies ) *
253+
dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j, i+numSecondarySpecies ) *
257254
dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration *
258255
params.mobileSecondarySpeciesFlag( j );
259256
}

‎src/reactions/massActions/unitTests/testMassActions.cpp‎

Lines changed: 16 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -45,13 +45,13 @@ void test_calculateLogSecondarySpeciesConcentration_helper()
4545
static constexpr int numPrimarySpecies = carbonateSystemAllEquilibrium.numPrimarySpecies();
4646
static constexpr int numSecondarySpecies = carbonateSystemAllEquilibrium.numSecondarySpecies();
4747

48-
CalculateLogSecondarySpeciesConcentrationData<numPrimarySpecies, numSecondarySpecies> data;
48+
CalculateLogSecondarySpeciesConcentrationData< numPrimarySpecies, numSecondarySpecies > data;
4949

5050
pmpl::genericKernelWrapper( 1, &data, [] HPCREACT_DEVICE ( auto * const dataCopy )
5151
{
5252
calculateLogSecondarySpeciesConcentration< double,
53-
int,
54-
int >( carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
53+
int,
54+
int >( carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
5555
dataCopy->logPrimarySpeciesSolution,
5656
dataCopy->logSecondarySpeciesConcentrations );
5757

@@ -60,11 +60,10 @@ void test_calculateLogSecondarySpeciesConcentration_helper()
6060
calculateLogSecondarySpeciesConcentrationWrtLogC< double,
6161
int,
6262
int >( carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
63-
dataCopy->logPrimarySpeciesSolution,
64-
dataCopy->logSecondarySpeciesConcentrations,
65-
dataCopy->dLogSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentrations );
66-
});
67-
63+
dataCopy->logPrimarySpeciesSolution,
64+
dataCopy->logSecondarySpeciesConcentrations,
65+
dataCopy->dLogSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentrations );
66+
} );
6867

6968

7069

@@ -126,13 +125,13 @@ struct CalculateAggregatePrimaryConcentrationsWrtLogCHelperData
126125
{
127126
double const primarySpeciesSolution[numPrimarySpecies] =
128127
{
129-
log(0.00043969547214915125),
130-
log(0.00037230096984514874),
131-
log(0.014716565308128551),
132-
log(0.0024913722747387217),
133-
log(1.8586090945989489),
134-
log(0.009881874292035079),
135-
log(1.0723078278653704)
128+
log( 0.00043969547214915125 ),
129+
log( 0.00037230096984514874 ),
130+
log( 0.014716565308128551 ),
131+
log( 0.0024913722747387217 ),
132+
log( 1.8586090945989489 ),
133+
log( 0.009881874292035079 ),
134+
log( 1.0723078278653704 )
136135
};
137136

138137
double aggregatePrimarySpeciesConcentration[numPrimarySpecies] = {0};
@@ -144,15 +143,15 @@ void testcalculateAggregatePrimaryConcentrationsWrtLogCHelper()
144143
{
145144
static constexpr int numPrimarySpecies = carbonateSystemAllEquilibrium.numPrimarySpecies();
146145

147-
CalculateAggregatePrimaryConcentrationsWrtLogCHelperData<numPrimarySpecies> data;
146+
CalculateAggregatePrimaryConcentrationsWrtLogCHelperData< numPrimarySpecies > data;
148147

149148
pmpl::genericKernelWrapper( 1, &data, [] HPCREACT_DEVICE ( auto * const dataCopy )
150149
{
151150
calculateAggregatePrimaryConcentrationsWrtLogC< double, int, int >( carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
152151
dataCopy->primarySpeciesSolution,
153152
dataCopy->aggregatePrimarySpeciesConcentration,
154153
dataCopy->dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations );
155-
});
154+
} );
156155

157156
double const expectedAggregatePrimarySpeciesConcentration[numPrimarySpecies] =
158157
{

‎src/reactions/reactionsSystems/Parameters.hpp‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -157,7 +157,7 @@ struct MixedReactionsParameters
157157

158158
HPCREACT_HOST_DEVICE static constexpr IndexType numSecondarySpecies() { return NUM_EQ_REACTIONS; }
159159

160-
HPCREACT_HOST_DEVICE
160+
HPCREACT_HOST_DEVICE
161161
constexpr
162162
EquilibriumReactionsParameters< RealType, IntType, IndexType, numSpecies(), numEquilibriumReactions() >
163163
equilibriumReactionsParameters() const
@@ -179,7 +179,7 @@ struct MixedReactionsParameters
179179
return { eqMatrix, eqConstants, mobileSpeciesFlags };
180180
}
181181

182-
HPCREACT_HOST_DEVICE
182+
HPCREACT_HOST_DEVICE
183183
constexpr
184184
KineticReactionsParameters< RealType, IntType, IndexType, numSpecies(), numKineticReactions() >
185185
kineticReactionsParameters() const
@@ -203,7 +203,7 @@ struct MixedReactionsParameters
203203
return { kineticMatrix, rateConstantForward, rateConstantReverse, equilibriumConstant, m_reactionRatesUpdateOption };
204204
}
205205

206-
HPCREACT_HOST_DEVICE
206+
HPCREACT_HOST_DEVICE
207207
void verifyParameterConsistency()
208208
{
209209
static constexpr int num_digits = 12;
@@ -239,10 +239,10 @@ struct MixedReactionsParameters
239239
}
240240
}
241241

242-
HPCREACT_HOST_DEVICE RealType stoichiometricMatrix( IndexType const r, int const i ) const { return m_stoichiometricMatrix[r][i]; }
243-
HPCREACT_HOST_DEVICE RealType equilibriumConstant( IndexType const r ) const { return m_equilibriumConstant[r]; }
244-
HPCREACT_HOST_DEVICE RealType rateConstantForward( IndexType const r ) const { return m_rateConstantForward[r]; }
245-
HPCREACT_HOST_DEVICE RealType rateConstantReverse( IndexType const r ) const { return m_rateConstantReverse[r]; }
242+
HPCREACT_HOST_DEVICE RealType stoichiometricMatrix( IndexType const r, int const i ) const { return m_stoichiometricMatrix[r][i]; }
243+
HPCREACT_HOST_DEVICE RealType equilibriumConstant( IndexType const r ) const { return m_equilibriumConstant[r]; }
244+
HPCREACT_HOST_DEVICE RealType rateConstantForward( IndexType const r ) const { return m_rateConstantForward[r]; }
245+
HPCREACT_HOST_DEVICE RealType rateConstantReverse( IndexType const r ) const { return m_rateConstantReverse[r]; }
246246

247247
CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > m_stoichiometricMatrix;
248248
CArrayWrapper< RealType, NUM_REACTIONS > m_equilibriumConstant;

‎src/reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ REAL_TYPE tolerance( REAL_TYPE const a, REAL_TYPE const b )
3535
* @tparam numSpecies Number of species.
3636
*/
3737
template< int numReactions, int numSpecies >
38-
struct ComputeResidualAndJacobianTestData
38+
struct ComputeResidualAndJacobianTestData
3939
{
4040
/// The reaction residuals
4141
double residual[numReactions] = { 0.0 };
@@ -65,23 +65,23 @@ void computeResidualAndJacobianTest( PARAMS_DATA const & params,
6565

6666
double const temperature = 298.15;
6767

68-
ComputeResidualAndJacobianTestData<numReactions, numSpecies> data;
68+
ComputeResidualAndJacobianTestData< numReactions, numSpecies > data;
6969
for( int i = 0; i < numSpecies; ++i )
7070
{
7171
data.speciesConcentration[i] = initialSpeciesConcentration[i];
72-
}
72+
}
7373

7474
pmpl::genericKernelWrapper( 1, &data, [params, temperature] HPCREACT_DEVICE ( auto * const dataCopy )
75-
{
76-
double xi[numReactions] = { 0.0 };
75+
{
76+
double xi[numReactions] = { 0.0 };
7777

78-
EquilibriumReactionsType::computeResidualAndJacobianReactionExtents( temperature,
79-
params,
80-
dataCopy->speciesConcentration,
81-
xi,
82-
dataCopy->residual,
83-
dataCopy->jacobian );
84-
});
78+
EquilibriumReactionsType::computeResidualAndJacobianReactionExtents( temperature,
79+
params,
80+
dataCopy->speciesConcentration,
81+
xi,
82+
dataCopy->residual,
83+
dataCopy->jacobian );
84+
} );
8585

8686
// printf( "R = { %8.4g, %8.4g }\n", residual[0], residual[1] );
8787
for( int r=0; r<numReactions; ++r )
@@ -114,7 +114,7 @@ struct TestEnforceEquilibriumData
114114
{
115115
/// The initial species concentrations
116116
double speciesConcentration0[numSpecies];
117-
117+
118118
/// The final species concentrations
119119
double speciesConcentration[numSpecies];
120120
};
@@ -134,19 +134,19 @@ void testEnforceEquilibrium( PARAMS_DATA const & params,
134134

135135
double const temperature = 298.15;
136136

137-
TestEnforceEquilibriumData<numSpecies> data;
137+
TestEnforceEquilibriumData< numSpecies > data;
138138
for( int i = 0; i < numSpecies; ++i )
139139
{
140140
data.speciesConcentration0[i] = initialSpeciesConcentration[i];
141141
}
142142

143143
pmpl::genericKernelWrapper( 1, &data, [params, temperature] HPCREACT_DEVICE ( auto * const dataCopy )
144-
{
145-
EquilibriumReactionsType::enforceEquilibrium_Extents( temperature,
146-
params,
147-
dataCopy->speciesConcentration0,
148-
dataCopy->speciesConcentration );
149-
});
144+
{
145+
EquilibriumReactionsType::enforceEquilibrium_Extents( temperature,
146+
params,
147+
dataCopy->speciesConcentration0,
148+
dataCopy->speciesConcentration );
149+
} );
150150

151151
for( int r=0; r<numSpecies; ++r )
152152
{

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