Added dipole-dipole interactions. #136
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mlund
reviewed
May 27, 2019
| if (type == "qpotential") | ||
| selfenergy_prefactor = 0.5; | ||
|
|
||
| selfenergy_ion_prefactor = 0.0; |
src/energy.cpp
Outdated
| @@ -344,6 +397,7 @@ Hamiltonian::Hamiltonian(Space &spc, const json &j) { | |||
| using namespace Potential; | |||
|
|
|||
| typedef CombinedPairPotential<CoulombGalore, LennardJones> CoulombLJ; | |||
| typedef CombinedPairPotential<DipoleDipoleGalore, LennardJones> Stockmayer; | |||
There was a problem hiding this comment.
is this needed? Just use nonbonded_exact ?
src/multipole.h
Outdated
| /** | ||
| * @brief Help-function for `sfQpotential` using order 3. | ||
| */ | ||
| inline void _DipoleDipoleQ2Help_3(double &a3, double &b3, double q) { |
There was a problem hiding this comment.
function names should be "camelCase", i.e. dipoleDipoleQ2Help3
| template <class Titer> double monopoleMoment(Titer begin, Titer end) { | ||
| double z = 0; | ||
| for (auto it = begin; it != end; ++it) | ||
| z += it->charge; | ||
| return z; | ||
| } //!< Calculates dipole moment vector for a set of particles | ||
|
|
||
| /** |
| @@ -82,21 +82,21 @@ void Faunus::Potential::CoulombGalore::sfQpotential(const Faunus::json &j) { | |||
| order = j.value("order", 300); | |||
| table = sf.generate([&](double q) { return qPochhammerSymbol(q, 1, order); }, 0, 1); | |||
| calcDielectric = [&](double M2V) { return 1 + 3 * M2V; }; | |||
| selfenergy_prefactor = 0.5; | |||
| selfenergy_prefactor = -1.0; | |||
There was a problem hiding this comment.
document self energies in md files?
|
This PR relates to issue #135. |
mlund
reviewed
May 27, 2019
| @@ -58,7 +58,7 @@ void EwaldData::update(const Point &box) { | |||
| factor *= 2; | |||
| double dkz2 = double(kz * kz); | |||
| Point kv = 2 * pc::pi * Point(kx / L.x(), ky / L.y(), kz / L.z()); | |||
| double k2 = kv.dot(kv); | |||
| double k2 = kv.dot(kv) + kappa2; // last term is only for Yukawa-Ewald | |||
src/potentials.cpp
Outdated
| } | ||
|
|
||
| catch (std::exception &e) { | ||
| std::cerr << "DipoleDipoleGalore error: " << e.what(); |
There was a problem hiding this comment.
use instead throw std::runtime_error(name + ": " + e.what());
src/potentials.cpp
Outdated
| j["type"] = type; | ||
| if (type == "wolf" || type == "fennell" || type == "ewald") | ||
| j["alpha"] = alpha; | ||
| if (type == "qpotential" || type == "q2potential") |
| Particle a = atoms[0]; | ||
| Particle b = atoms[1]; | ||
| Point r = {2, 0, 0}; | ||
| CHECK(u(a, a, r) == Approx(dipoledipole(a, a, r))); // interaction between two parallell dipoles, directed parallell to their seperation |
There was a problem hiding this comment.
this checks if FunctorPotential gives same results as dipoledipole. Add test that compares with precalculated values? (probably for some less idealized dipole orientations)
src/potentials.h
Outdated
| using doctest::Approx; | ||
|
|
||
| json j = R"({ "atomlist" : [ | ||
| {"A": { "mu":[3.0,0.0,0.0] }}, |
There was a problem hiding this comment.
according to documentation, mu should be a unit vector
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Please check that:
make all pyfaunus usagetips unittests testpasses with no errorsthere are no compiler warnings
no temporary files (.o, .pqr, state etc) are included in the commit
naming policies for classes, functions, and variables adhere to:
source files use soft-indendation of four. To setup automatic
code formatting of proposed changes using
clang-format, installthe provided git commit hook: