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Document FQ feature
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‎CHANGELOG.md‎

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@@ -4,6 +4,7 @@
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### Added
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- An implementation of the fluctuating charge (FQ) molecular mechanics (MM) model.
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- A new API initialization function `pcmsolver_new_read_host`. This allows
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creating an *uninitialized* `pcmsolver_context_t` object: the initialization is
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deferred to a later point and orchestrated by the host program. The input

‎doc/snippets/example_input-all.inp‎

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@@ -44,3 +44,8 @@ ChargeDistribution {
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Monopoles = [Double]
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Dipoles = [Double]
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}
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MMFQ {
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SitesPerFragment = [Integer]
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Sites = [Array of Doubles]
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NonPolarizable = [Bool]
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}

‎doc/users/input.rst‎

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@@ -485,6 +485,33 @@ No additional spheres will be generated.
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* **Type**: array of doubles
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MMFQ section keywords
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---------------------
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Set a classical fluctuating charge force field. This is incompatible with any
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options specifying a continuum model. No additional spheres will be generated.
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.. glossary::
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SitesPerFragment
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Number of sites per MM fragment. For water this is 3.
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* **Type**: integer
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* **Default**: 3
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Sites
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Array of MM sites for the FQ model
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Format is :math:`[\ldots, x_i, y_i, z_i, chi_i, eta_i \ldots]`
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* **Type**: array of doubles
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NonPolarizable
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Whether to make this force field nonpolarizable.
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* **Type**: bool
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* **Default**: false
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.. _available-radii:
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Available radii

‎src/interface/Input.cpp‎

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@@ -435,9 +435,7 @@ std::string right_trim(const char * src) {
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return right_trim(tmp);
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}
437437

438-
std::string trim(std::string s) {
439-
return right_trim(left_trim(s));
440-
}
438+
std::string trim(std::string s) { return right_trim(left_trim(s)); }
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std::string trim(const char * src) {
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std::string tmp(src);

‎src/interface/Meddle.cpp‎

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@@ -155,16 +155,16 @@ void Meddle::CTORBody() {
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TIMER_ON("Meddle::initCavity");
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initCavity();
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TIMER_OFF("Meddle::initCavity");
158-
}
159158

160-
TIMER_ON("Meddle::initStaticSolver");
161-
initStaticSolver();
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TIMER_OFF("Meddle::initStaticSolver");
159+
TIMER_ON("Meddle::initStaticSolver");
160+
initStaticSolver();
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TIMER_OFF("Meddle::initStaticSolver");
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164-
if (input_.isDynamic()) {
165-
TIMER_ON("Meddle::initDynamicSolver");
166-
initDynamicSolver();
167-
TIMER_OFF("Meddle::initDynamicSolver");
163+
if (input_.isDynamic()) {
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TIMER_ON("Meddle::initDynamicSolver");
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initDynamicSolver();
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TIMER_OFF("Meddle::initDynamicSolver");
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}
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}
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}
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@@ -175,6 +175,7 @@ Meddle::Meddle(const Input & input, const HostWriter & write)
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cavity_(nullptr),
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K_0_(nullptr),
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K_d_(nullptr),
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FQ_(nullptr),
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hasDynamic_(false),
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hasFQ_(false) {
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input_.initMolecule();
@@ -188,6 +189,7 @@ Meddle::Meddle(const std::string & inputFileName, const HostWriter & write)
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cavity_(nullptr),
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K_0_(nullptr),
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K_d_(nullptr),
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FQ_(nullptr),
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hasDynamic_(false),
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hasFQ_(false) {
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input_.initMolecule();
@@ -206,6 +208,7 @@ Meddle::Meddle(int nr_nuclei,
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cavity_(nullptr),
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K_0_(nullptr),
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K_d_(nullptr),
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FQ_(nullptr),
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hasDynamic_(false),
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hasFQ_(false) {
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TIMER_ON("Meddle::initInput");
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cavity_(nullptr),
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K_0_(nullptr),
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K_d_(nullptr),
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FQ_(nullptr),
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hasDynamic_(false),
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hasFQ_(false) {
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TIMER_ON("Meddle::initInput");
@@ -247,6 +251,7 @@ Meddle::Meddle(int nr_nuclei,
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cavity_(nullptr),
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K_0_(nullptr),
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K_d_(nullptr),
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FQ_(nullptr),
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hasDynamic_(false),
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hasFQ_(false) {
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// This one does a deferred initialization:

‎src/mmfq/FQOhno.cpp‎

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@@ -1,6 +1,6 @@
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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
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* Copyright (C) 2020 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*
@@ -76,7 +76,8 @@ Eigen::VectorXd FQOhno::computeCharge_impl(const Eigen::VectorXd & potential,
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std::ostream & FQOhno::printSolver(std::ostream & os) {
7878
os << "Fluctuating charge solver type: Ohno" << std::endl;
79-
if (nonPolarizable_) os << "Nonpolarizable force field" << std::endl;
79+
if (nonPolarizable_)
80+
os << "Nonpolarizable force field" << std::endl;
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os << "Number of fragments = " << mmfq_.nFragments << std::endl;
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os << "Number of sites per fragment = " << mmfq_.nSitesPerFragment << std::endl;
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os << "Number of sites = " << mmfq_.nFragments * mmfq_.nSitesPerFragment;

‎src/mmfq/FQOhno.hpp‎

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/*
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2017 Roberto Di Remigio, Luca Frediani and collaborators.
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* Copyright (C) 2020 Roberto Di Remigio, Luca Frediani and collaborators.
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*
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* This file is part of PCMSolver.
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*

‎src/utils/MMFQ.hpp‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
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* Copyright (C) 2020 Roberto Di Remigio, Luca Frediani and contributors.
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*
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* This file is part of PCMSolver.
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*

‎tests/CMakeLists.txt‎

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@@ -18,16 +18,17 @@ target_compile_definitions(unit_tests
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"$<$<NOT:$<BOOL:${HAS_CXX11}>>:CATCH_CONFIG_NO_CPP11>"
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)
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21-
add_subdirectory(input)
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add_subdirectory(numerical_quadrature)
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add_subdirectory(gepol)
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add_subdirectory(dielectric_profile)
25-
add_subdirectory(green)
21+
add_subdirectory(benchmark)
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add_subdirectory(bi_operators)
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add_subdirectory(cpcm)
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add_subdirectory(dielectric_profile)
25+
add_subdirectory(gepol)
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add_subdirectory(green)
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add_subdirectory(iefpcm)
28+
add_subdirectory(input)
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add_subdirectory(mmfq)
30+
add_subdirectory(numerical_quadrature)
2931
add_subdirectory(utils)
30-
add_subdirectory(benchmark)
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3233
target_link_libraries(unit_tests
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PRIVATE

‎tests/green/AnalyticEvaluate.hpp‎

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@@ -396,23 +396,33 @@ inline Eigen::Array4d analyticSphericalSharp(double eps,
396396
// Value of the function
397397
result(0) = 1.0 / (epsSolv * distance) - G_img;
398398

399-
double d_probe_G_img = sevenPointStencil(
400-
std::bind(
401-
imagePotential, eps, epsSolv, radius, origin, maxL, std::placeholders::_1, std::placeholders::_2),
402-
pp,
403-
sp,
404-
ppNormal,
405-
1.0e-04);
399+
double d_probe_G_img = sevenPointStencil(std::bind(imagePotential,
400+
eps,
401+
epsSolv,
402+
radius,
403+
origin,
404+
maxL,
405+
std::placeholders::_1,
406+
std::placeholders::_2),
407+
pp,
408+
sp,
409+
ppNormal,
410+
1.0e-04);
406411
// Value of the directional derivative wrt probe
407412
result(1) = (sp - pp).dot(ppNormal) / (epsSolv * distance_3) - d_probe_G_img;
408413

409-
double d_source_G_img = sevenPointStencil(
410-
std::bind(
411-
imagePotential, eps, epsSolv, radius, origin, maxL, std::placeholders::_1, std::placeholders::_2),
412-
sp,
413-
pp,
414-
spNormal,
415-
1.0e-04);
414+
double d_source_G_img = sevenPointStencil(std::bind(imagePotential,
415+
eps,
416+
epsSolv,
417+
radius,
418+
origin,
419+
maxL,
420+
std::placeholders::_1,
421+
std::placeholders::_2),
422+
sp,
423+
pp,
424+
spNormal,
425+
1.0e-04);
416426
// Directional derivative wrt source
417427
result(2) = -(sp - pp).dot(spNormal) / (epsSolv * distance_3) - d_source_G_img;
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// Value of the Hessian

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