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Add CheckSpecies module #366

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merged 17 commits into from Sep 15, 2020
Merged

Add CheckSpecies module #366

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653d15c
Add general integer/string tuple vector keyword.
trisyoungs Sep 2, 2020
badf5f8
Add CheckSpecies module with basic atom type test.
trisyoungs Sep 2, 2020
3e6624d
Add general integer/double tuple vector keyword.
trisyoungs Sep 2, 2020
8c413a7
Add checking of intramolecular bond parameters.
trisyoungs Sep 2, 2020
9bea323
Add access to higher-order intramolecular terms by atom index.
trisyoungs Sep 2, 2020
0aa1145
Add checking of other intramolecular term parameters.
trisyoungs Sep 2, 2020
123e913
Add separating blank line.
trisyoungs Sep 2, 2020
f76b1a2
Don't use asterisks in type names.
trisyoungs Sep 4, 2020
4f57cd9
Update neta system test to be more comprehensive.
trisyoungs Sep 2, 2020
1a86eff
Minor formatting.
trisyoungs Sep 4, 2020
3253cf8
Remove needless comments
trisyoungs Sep 9, 2020
7bb80d2
Fix formatting.
trisyoungs Sep 10, 2020
ebf67a2
Rename source files for new classes.
trisyoungs Sep 10, 2020
f92f5cb
Use std::optional for required value count.
trisyoungs Sep 10, 2020
0cd03e8
Remove unnecessary comments.
trisyoungs Sep 10, 2020
e744e07
Reimplement and condense parameter testing.
trisyoungs Sep 10, 2020
153ce43
Include <optional>.
trisyoungs Sep 10, 2020
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1 change: 1 addition & 0 deletions CMakeLists.txt
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Expand Up @@ -209,6 +209,7 @@ set(BASIC_LINK_LIBS
calculatesdfmodule
calibrationmodule
checksmodule
checkspeciesmodule
datatestmodule
energymodule
epsrmodule
Expand Down
8 changes: 7 additions & 1 deletion src/classes/species.h
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Expand Up @@ -191,6 +191,8 @@ class Species : public ListItem<Species>, public ObjectStore<Species>
bool hasAngle(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k) const;
// Return the SpeciesAngle between the specified SpeciesAtoms
OptionalReferenceWrapper<SpeciesAngle> getAngle(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k);
// Return the SpeciesAngle between the specified SpeciesAtom indices
OptionalReferenceWrapper<SpeciesAngle> getAngle(int i, int j, int k);
// Add new SpeciesTorsion definition (from SpeciesAtom*)
SpeciesTorsion &addTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l);
// Add new SpeciesTorsion definition
Expand All @@ -205,6 +207,8 @@ class Species : public ListItem<Species>, public ObjectStore<Species>
bool hasTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l) const;
// Return the SpeciesTorsion between the specified SpeciesAtoms
OptionalReferenceWrapper<SpeciesTorsion> getTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l);
// Return the SpeciesTorsion between the specified SpeciesAtom indices
OptionalReferenceWrapper<SpeciesTorsion> getTorsion(int i, int j, int k, int l);
// Add new SpeciesImproper definition (from SpeciesAtom*)
SpeciesImproper &addImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l);
// Add new SpeciesImproper definition
Expand All @@ -218,7 +222,9 @@ class Species : public ListItem<Species>, public ObjectStore<Species>
// Return whether SpeciesImproper between SpeciesAtoms exists
bool hasImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l) const;
// Return the SpeciesImproper between the specified SpeciesAtoms (if it exists)
OptionalReferenceWrapper<SpeciesImproper> improper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l);
OptionalReferenceWrapper<SpeciesImproper> getImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l);
// Return the SpeciesImproper between the specified SpeciesAtom indices
OptionalReferenceWrapper<SpeciesImproper> getImproper(int i, int j, int k, int l);
// Return whether the attached atoms lists have been created
bool attachedAtomListsGenerated() const;
// Generate attached Atom lists for all intramolecular terms
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38 changes: 28 additions & 10 deletions src/classes/species_intra.cpp
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Expand Up @@ -277,15 +277,10 @@ OptionalReferenceWrapper<SpeciesAngle> Species::getAngle(SpeciesAtom *i, Species
return *it;
}

// Return the SpeciesTorsion between the specified SpeciesAtoms
OptionalReferenceWrapper<SpeciesTorsion> Species::getTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l)
// Return the SpeciesAngle between the specified SpeciesAtom indic
OptionalReferenceWrapper<SpeciesAngle> Species::getAngle(int i, int j, int k)
{
auto it =
std::find_if(torsions_.begin(), torsions_.end(), [i, j, k, l](auto &torsion) { return torsion.matches(i, j, k, l); });
if (it == torsions_.end())
return {};

return *it;
return getAngle(atoms_[i], atoms_[j], atoms_[k]);
}

// Add new SpeciesTorsion definition (from supplied SpeciesAtom pointers)
Expand Down Expand Up @@ -331,6 +326,23 @@ bool Species::hasTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, Species
return it != torsions_.end();
}

// Return the SpeciesTorsion between the specified SpeciesAtoms
OptionalReferenceWrapper<SpeciesTorsion> Species::getTorsion(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l)
{
auto it =
std::find_if(torsions_.begin(), torsions_.end(), [i, j, k, l](auto &torsion) { return torsion.matches(i, j, k, l); });
if (it == torsions_.end())
return {};

return *it;
}

// Return the SpeciesTorsion between the specified SpeciesAtom indices
OptionalReferenceWrapper<SpeciesTorsion> Species::getTorsion(int i, int j, int k, int l)
{
return getTorsion(atoms_[i], atoms_[j], atoms_[k], atoms_[l]);
}

// Add new SpeciesImproper definition (from SpeciesAtom*)
SpeciesImproper &Species::addImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l)
{
Expand All @@ -340,7 +352,7 @@ SpeciesImproper &Species::addImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAto
Messenger::warn("Refused to add a new Improper between atoms {}, {}, {} and {} in Species '{}' since it "
"already exists.\n",
i->userIndex(), j->userIndex(), k->userIndex(), l->userIndex(), name_);
return *improper(i, j, k, l);
return *getImproper(i, j, k, l);
}

// OK to add new improper
Expand Down Expand Up @@ -378,7 +390,7 @@ bool Species::hasImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, Specie
}

// Return the SpeciesImproper between the specified SpeciesAtoms (if it exists)
OptionalReferenceWrapper<SpeciesImproper> Species::improper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l)
OptionalReferenceWrapper<SpeciesImproper> Species::getImproper(SpeciesAtom *i, SpeciesAtom *j, SpeciesAtom *k, SpeciesAtom *l)
{
auto it = std::find_if(impropers_.begin(), impropers_.end(),
[i, j, k, l](auto &improper) { return improper.matches(i, j, k, l); });
Expand All @@ -388,6 +400,12 @@ OptionalReferenceWrapper<SpeciesImproper> Species::improper(SpeciesAtom *i, Spec
return *it;
}

// Return the SpeciesImproper between the specified SpeciesAtom indices
OptionalReferenceWrapper<SpeciesImproper> Species::getImproper(int i, int j, int k, int l)
{
return getImproper(atoms_[i], atoms_[j], atoms_[k], atoms_[l]);
}

// Return whether the attached atoms lists have been created
bool Species::attachedAtomListsGenerated() const { return attachedAtomListsGenerated_; }

Expand Down
2 changes: 1 addition & 1 deletion src/data/ff.cpp
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Expand Up @@ -515,7 +515,7 @@ bool Forcefield::assignIntramolecular(Species *sp, int flags) const
const ForcefieldImproperTerm &term = *optTerm;
// Check to see if the Species already has an improper definition - if
// not create one
auto improper = sp->improper(i, j, k, l);
auto improper = sp->getImproper(i, j, k, l);
if (!improper)
improper = sp->addImproper(i, j, k, l);

Expand Down
9 changes: 5 additions & 4 deletions src/data/ff/oplsaa2005/atomtypes.cpp
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Expand Up @@ -29,6 +29,7 @@
* Notes:
* Epsilon values have been converted from kcal to kJ.
* Any inconsistencies between the forcefield as implemented here and the original work are the sole responsibility of TGAY.
* Atom types containing '*' (e.g. 'C*', 'N*') are renamed to use '^' as '*' represents a wildcard match in the name.
*
* References:
* W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225-11236 (1996).
Expand Down Expand Up @@ -527,7 +528,7 @@ OptionalReferenceWrapper<const ForcefieldAtomType> OPLSAA2005BaseForcefield::opl
{this, ELEMENT_O, 497, "OY_a", "", "sulfoxide - all atom", -0.420000, 1.171520, 2.930000},
{this, ELEMENT_C, 498, "CT", "", "CH3 all-atom C: sulfoxide", -0.035000, 0.276144, 3.500000},
{this, ELEMENT_C, 499, "CT", "", "CH2 all-atom C: sulfoxide", 0.025000, 0.276144, 3.500000},
{this, ELEMENT_C, 500, "Cstar", "", "CG in TRP", 0.075000, 0.292880, 3.550000},
{this, ELEMENT_C, 500, "C^", "", "CG in TRP", 0.075000, 0.292880, 3.550000},
{this, ELEMENT_C, 501, "CB", "", "CD C in TRP", -0.055000, 0.292880, 3.550000},
{this, ELEMENT_C, 502, "CN", "", "CE C in TRP", 0.130000, 0.292880, 3.550000},
{this, ELEMENT_N, 503, "NA", "", "NE in TRP", -0.570000, 0.711280, 3.250000},
Expand Down Expand Up @@ -855,9 +856,9 @@ OptionalReferenceWrapper<const ForcefieldAtomType> OPLSAA2005BaseForcefield::opl
{this, ELEMENT_C, 933, "CO", "", "C1' of (ura, thy) by Deping", 0.510000, 0.276144, 3.500000},
{this, ELEMENT_O, 934, "OH_a", "", "O5' by Deping", -0.655000, 0.711280, 3.120000},
{this, ELEMENT_H, 935, "HO", "", "H(3') OH by Deping", 0.390000, 0.000000, 0.000000},
{this, ELEMENT_N, 936, "N*", "", "Adenine N9 Guanine nucleosides", -0.500000, 0.711280, 3.250000},
{this, ELEMENT_N, 937, "N*", "", "Cytosine N1 nucleoside", -0.560000, 0.711280, 3.250000},
{this, ELEMENT_N, 938, "N*", "", "Uracil N1 Thymine nucleosides", -0.600000, 0.711280, 3.250000},
{this, ELEMENT_N, 936, "N^", "", "Adenine N9 Guanine nucleosides", -0.500000, 0.711280, 3.250000},
{this, ELEMENT_N, 937, "N^", "", "Cytosine N1 nucleoside", -0.560000, 0.711280, 3.250000},
{this, ELEMENT_N, 938, "N^", "", "Uracil N1 Thymine nucleosides", -0.600000, 0.711280, 3.250000},
{this, ELEMENT_C, 939, "CZ_a", "", "alkyne RC%CR - only did MC for MeCCMe", 0.000000, 0.878640, 3.300000},
{this, ELEMENT_N, 940, "N3", "", "N (R3NH+)", -0.100000, 0.711280, 3.250000},
{this, ELEMENT_H, 941, "H3", "", "H (R3NH+)", 0.290000, 0.000000, 0.000000},
Expand Down