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Correctness testing with TOML #1682

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merged 12 commits into from
Nov 3, 2023
Merged

Correctness testing with TOML #1682

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2c1d367
Fix import of node name when deserialising
rprospero Oct 23, 2023
c8d6ba6
Run the conformance test on the imported TOML data
rprospero Oct 23, 2023
7ab06c3
Add setup and prepare to full toml test
rprospero Oct 24, 2023
325d3f5
Correctly serialise force charge parameter
rprospero Oct 24, 2023
e9fae8b
Fix charge handling in serialisation
rprospero Oct 24, 2023
64185fd
Merge branch 'develop' into TOML_Full_Test
rprospero Oct 26, 2023
0393e63
Fix whitespace
rprospero Oct 26, 2023
62be5c6
Properly clear dummy dissolve before loading config file
rprospero Oct 31, 2023
9fb0d7e
Better variable names
rprospero Nov 2, 2023
4d96779
Charge autoChargeSource default
rprospero Nov 2, 2023
81c5b52
Less boilerplate in TOML for pair potentials
rprospero Nov 2, 2023
326ae8d
Fix whitespace
rprospero Nov 2, 2023
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12 changes: 8 additions & 4 deletions src/classes/serializablePairPotential.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@

#include "classes/serializablePairPotential.h"

SerializablePairPotential::SerializablePairPotential(double &range, double &delta, bool &source,
std::vector<std::shared_ptr<AtomType>> &types)
: range_(range), delta_(delta), atomTypeChargeSource_(source), atomTypes_(types),
coulombTruncationScheme_(PairPotential::coulombTruncationScheme_),
SerializablePairPotential::SerializablePairPotential(double &range, double &delta, bool &source, bool &forceCharge,
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Do we still need the SerializablePairPotential class? It feels like its just wrapping functionality that could be added into Dissolve::serialise() and Dissolve::deserialise()...

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I agree that we need to review SerializablePairPotential, as I'm increasingly unhappy with the design. However, I'm not sure that Dissolve is the right place for it, either. I'll add an issue for it and we can review that before the final TOML addition.

bool &autoCharge, std::vector<std::shared_ptr<AtomType>> &types)
: range_(range), delta_(delta), atomTypeChargeSource_(source), atomTypes_(types), forceCharge_(forceCharge),
autoCharge_(autoCharge), coulombTruncationScheme_(PairPotential::coulombTruncationScheme_),
shortRangeTruncationScheme_(PairPotential::shortRangeTruncationScheme_){};

double &SerializablePairPotential::range() { return range_; }
Expand Down Expand Up @@ -44,6 +44,8 @@ SerialisedValue SerializablePairPotential::serialise() const
{"range", range_},
{"delta", delta_},
{"includeCoulomb", atomTypeChargeSource_},
{"forceChargeSource", forceCharge_},
{"autoChargeSource", autoCharge_},
{"coulombTruncation", PairPotential::coulombTruncationSchemes().serialise(coulombTruncationScheme_)},
{"shortRangeTruncation", PairPotential::shortRangeTruncationSchemes().serialise(shortRangeTruncationScheme_)}};
for (auto &atomType : atomTypes_)
Expand All @@ -57,6 +59,8 @@ void SerializablePairPotential::deserialise(const SerialisedValue &node)
range_ = toml::find_or<double>(node, "range", 15.0);
delta_ = toml::find_or<double>(node, "delta", 0.005);
atomTypeChargeSource_ = toml::find_or<bool>(node, "includeCoulomb", false);
forceCharge_ = toml::find_or<bool>(node, "forceChargeSource", false);
autoCharge_ = toml::find_or<bool>(node, "autoChargeSource", false);
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coulombTruncationScheme_ =
PairPotential::coulombTruncationSchemes().deserialise(toml::find_or<std::string>(node, "coulombTruncation", "Shifted"));
Expand Down
5 changes: 3 additions & 2 deletions src/classes/serializablePairPotential.h
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Expand Up @@ -15,7 +15,7 @@ class SerializablePairPotential : public Serialisable<>
private:
double &range_;
double &delta_;
bool &atomTypeChargeSource_;
bool &atomTypeChargeSource_, &forceCharge_, &autoCharge_;

std::vector<std::shared_ptr<AtomType>> &atomTypes_;

Expand All @@ -24,7 +24,8 @@ class SerializablePairPotential : public Serialisable<>

// AtomTypes
public:
SerializablePairPotential(double &range, double &delta, bool &source, std::vector<std::shared_ptr<AtomType>> &types);
SerializablePairPotential(double &range, double &delta, bool &source, bool &forceCharge, bool &autoCharge,
std::vector<std::shared_ptr<AtomType>> &types);

double &range();
const double &range() const;
Expand Down
4 changes: 2 additions & 2 deletions src/main/dissolve.cpp
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Expand Up @@ -8,8 +8,8 @@
#include "classes/species.h"

Dissolve::Dissolve(CoreData &coreData)
: coreData_(coreData),
serializablePairPotential_(pairPotentialRange_, pairPotentialDelta_, atomTypeChargeSource_, coreData_.atomTypes())
: coreData_(coreData), serializablePairPotential_(pairPotentialRange_, pairPotentialDelta_, atomTypeChargeSource_,
forceChargeSource_, automaticChargeSource_, coreData_.atomTypes())
{
// Set core simulation variables
restartFileFrequency_ = 10;
Expand Down
13 changes: 0 additions & 13 deletions src/main/io.cpp
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Expand Up @@ -127,13 +127,6 @@ SerialisedValue Dissolve::serialise() const
{
SerialisedValue root;

// If TOML is disabled,
if constexpr (!toml_testing_flag)
{
Messenger::error("This build does not support TOML.");
return root;
}

if (!coreData_.masterBonds().empty() || !coreData_.masterAngles().empty() || !coreData_.masterTorsions().empty() ||
!coreData_.masterImpropers().empty())
root["master"] = coreData_.serialiseMaster();
Expand All @@ -152,12 +145,6 @@ SerialisedValue Dissolve::serialise() const
// Read values from a serialisable value
void Dissolve::deserialise(const SerialisedValue &node)
{
// If TOML is disabled,
if constexpr (!toml_testing_flag)
{
Messenger::error("This build does not support TOML.");
return;
}

if (node.contains("pairPotentials"))
{
Expand Down
8 changes: 4 additions & 4 deletions tests/modules/avgMol.cpp
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Expand Up @@ -15,8 +15,8 @@ class AvgMolModuleWaterTest : public ::testing::Test

void SetUp() override
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/avgMol-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/avgMol-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));
}
};

Expand All @@ -33,7 +33,7 @@ class AvgMolModuleBendyTest : public ::testing::Test
protected:
DissolveSystemTest systemTest;

void SetUp() override { ASSERT_NO_THROW(systemTest.setUp("dissolve/input/avgMol-bendy.txt")); }
void SetUp() override { ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/avgMol-bendy.txt")); }

void checkCoordinates()
{
Expand All @@ -45,7 +45,7 @@ class AvgMolModuleBendyTest : public ::testing::Test

TEST_F(AvgMolModuleBendyTest, AverageCoordinates)
{
ASSERT_TRUE(systemTest.iterateRestart(201));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(201));

checkCoordinates();
}
Expand Down
4 changes: 2 additions & 2 deletions tests/modules/dAngle.cpp
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Expand Up @@ -15,8 +15,8 @@ class DAngleModuleTest : public ::testing::Test

TEST_F(DAngleModuleTest, Water)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/dAngle.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/dAngle.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

EXPECT_TRUE(systemTest.checkData1D(
"DAngle(X-H...O)//Process1D//RDF(BC)",
Expand Down
10 changes: 5 additions & 5 deletions tests/modules/epsr.cpp
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Expand Up @@ -58,7 +58,7 @@ class EPSRModuleTest : public ::testing::Test

TEST_F(EPSRModuleTest, Water3NInpA)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/epsr-water-inpa.txt"));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/epsr-water-inpa.txt"));
ASSERT_TRUE(systemTest.dissolve().iterate(1));

// Estimated Partials
Expand Down Expand Up @@ -107,7 +107,7 @@ TEST_F(EPSRModuleTest, Water3NInpA)

TEST_F(EPSRModuleTest, Water3NX)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/epsr-water-3n-x.txt"));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/epsr-water-3n-x.txt"));
ASSERT_TRUE(systemTest.dissolve().iterate(1));

// Test total neutron-weighted F(r)
Expand Down Expand Up @@ -138,7 +138,7 @@ TEST_F(EPSRModuleTest, Water3NX)

TEST_F(EPSRModuleTest, Benzene)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/epsr-benzene-3n.txt"));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/epsr-benzene-3n.txt"));
ASSERT_TRUE(systemTest.dissolve().iterate(1));

// Test total neutron-weighted F(r)
Expand Down Expand Up @@ -200,7 +200,7 @@ TEST_F(EPSRModuleTest, BenzeneReadPCof) { ASSERT_NO_THROW(systemTest.setUp("diss

TEST_F(EPSRModuleTest, ScatteringMatrix)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/epsr-5datasets.txt"));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/epsr-5datasets.txt"));
ASSERT_TRUE(systemTest.dissolve().iterate(1));

// Find EPSR module
Expand All @@ -221,7 +221,7 @@ TEST_F(EPSRModuleTest, ScatteringMatrix)

TEST_F(EPSRModuleTest, DataWeighting)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/epsr-5datasets-weighted.txt"));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/epsr-5datasets-weighted.txt"));
ASSERT_TRUE(systemTest.dissolve().iterate(1));

// Find EPSR module
Expand Down
4 changes: 2 additions & 2 deletions tests/modules/histogramCN.cpp
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Expand Up @@ -28,8 +28,8 @@ TEST_F(HistogramCNModuleTest, Simple)

TEST_F(HistogramCNModuleTest, Water)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/histogramCN-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/histogramCN-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

EXPECT_TRUE(systemTest.checkData1D(
"CN(COM-COM)//Process1D//Histogram",
Expand Down
4 changes: 2 additions & 2 deletions tests/modules/intraDistance.cpp
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Expand Up @@ -15,8 +15,8 @@ class IntraDistanceModuleTest : public ::testing::Test

TEST_F(IntraDistanceModuleTest, Water)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/intraDistance.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/intraDistance.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

EXPECT_TRUE(systemTest.checkData1D(
"D(O-H1)//Process1D//NormalisedHistogram",
Expand Down
4 changes: 2 additions & 2 deletions tests/modules/orientedSDF.cpp
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Expand Up @@ -15,8 +15,8 @@ class OrientedSDFModuleTest : public ::testing::Test

TEST_F(OrientedSDFModuleTest, Benzene)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/orientedSDF-benzene.txt"));
ASSERT_TRUE(systemTest.iterateRestart(80));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/orientedSDF-benzene.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(80));

EXPECT_TRUE(systemTest.checkData3D(
"OrientedSDF(R-R)//Process3D//SDF",
Expand Down
8 changes: 4 additions & 4 deletions tests/modules/sdf.cpp
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Expand Up @@ -16,8 +16,8 @@ class SDFModuleTest : public ::testing::Test

TEST_F(SDFModuleTest, Water)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/sdf-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/sdf-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

EXPECT_TRUE(systemTest.checkData3D(
"SDF(O)//Process3D//SDF",
Expand All @@ -26,8 +26,8 @@ TEST_F(SDFModuleTest, Water)

TEST_F(SDFModuleTest, Benzene)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/sdf-benzene.txt"));
ASSERT_TRUE(systemTest.iterateRestart(80));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/sdf-benzene.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(80));

EXPECT_TRUE(systemTest.checkData3D(
"SDF(R-R)//Process3D//SDF",
Expand Down
16 changes: 8 additions & 8 deletions tests/modules/siteRDF.cpp
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Expand Up @@ -15,8 +15,8 @@ class SiteRDFModuleTest : public ::testing::Test

TEST_F(SiteRDFModuleTest, Water)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/siteRDF-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/siteRDF-water.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

// O-O RDF
EXPECT_TRUE(systemTest.checkData1D(
Expand Down Expand Up @@ -53,8 +53,8 @@ TEST_F(SiteRDFModuleTest, Water)

TEST_F(SiteRDFModuleTest, WaterNPT)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/siteRDF-waterNPT.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/siteRDF-waterNPT.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

// O-O RDF
EXPECT_TRUE(systemTest.checkData1D(
Expand Down Expand Up @@ -83,8 +83,8 @@ TEST_F(SiteRDFModuleTest, WaterNPT)

TEST_F(SiteRDFModuleTest, WaterDynamic)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/siteRDF-waterDynamic.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/siteRDF-waterDynamic.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

// O-O RDF
EXPECT_TRUE(systemTest.checkData1D(
Expand All @@ -109,8 +109,8 @@ TEST_F(SiteRDFModuleTest, WaterDynamic)

TEST_F(SiteRDFModuleTest, WaterFragments)
{
ASSERT_NO_THROW(systemTest.setUp("dissolve/input/siteRDF-waterFragments.txt"));
ASSERT_TRUE(systemTest.iterateRestart(95));
ASSERT_NO_THROW(systemTest.setUp<TomlFailure>("dissolve/input/siteRDF-waterFragments.txt"));
ASSERT_TRUE(systemTest.iterateRestart<TomlFailure>(95));

// O-O RDF
EXPECT_TRUE(systemTest.checkData1D(
Expand Down
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