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Change function body for gradientProbe and gradientSource · PCMSolver/pcmsolver@c6b359b · GitHub

  1. PCMSolver
  2. pcmsolver

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Commit c6b359b

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Roberto Di Remigio
committed
Change function body for gradientProbe and gradientSource
1 parent bafd5b8 commit c6b359b

3 files changed

Lines changed: 64 additions & 86 deletions

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‎src/green/GreensFunction.hpp‎

Lines changed: 6 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -123,19 +123,10 @@ class GreensFunction: public IGreensFunction
123123
{
124124
Eigen::Vector3d gradient = Eigen::Vector3d::Zero();
125125

126-
DerivativeTraits t1[3], t2[3], grad;
127-
t1[0] = p1(0);
128-
t1[0][1] = 1;
129-
t1[1] = p1(1);
130-
t1[1][2] = 1;
131-
t1[2] = p1(2);
132-
t1[2][3] = 1;
133-
t2[0] = p2(0);
134-
t2[1] = p2(1);
135-
t2[2] = p2(2);
136-
grad = this->operator()(t1, t2);
126+
gradient(0) = derivativeSource(Eigen::Vector3d::UnitX(), p1, p2);
127+
gradient(1) = derivativeSource(Eigen::Vector3d::UnitY(), p1, p2);
128+
gradient(2) = derivativeSource(Eigen::Vector3d::UnitZ(), p1, p2);
137129

138-
gradient << grad[1], grad[2], grad[3];
139130
return gradient;
140131
}
141132
/*! Returns full gradient of Greens's function for the pair of points p1, p2:
@@ -149,19 +140,10 @@ class GreensFunction: public IGreensFunction
149140
{
150141
Eigen::Vector3d gradient = Eigen::Vector3d::Zero();
151142

152-
DerivativeTraits t1[3], t2[3], grad;
153-
t1[0] = p1(0);
154-
t1[1] = p1(1);
155-
t1[2] = p1(2);
156-
t2[0] = p2(0);
157-
t2[0][1] = 1;
158-
t2[1] = p2(1);
159-
t2[1][2] = 1;
160-
t2[2] = p2(2);
161-
t2[2][3] = 1;
162-
grad = this->operator()(t1, t2);
143+
gradient(0) = derivativeProbe(Eigen::Vector3d::UnitX(), p1, p2);
144+
gradient(1) = derivativeProbe(Eigen::Vector3d::UnitY(), p1, p2);
145+
gradient(2) = derivativeProbe(Eigen::Vector3d::UnitZ(), p1, p2);
163146

164-
gradient << grad[1], grad[2], grad[3];
165147
return gradient;
166148
}
167149

‎tests/bi_operators/bi_operators_collocation.cpp‎

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -43,9 +43,9 @@
4343
#include "GePolCavity.hpp"
4444
#include "CollocationIntegrator.hpp"
4545
#include "PhysicalConstants.hpp"
46-
#include "TanhSphericalDiffuse.hpp"
47-
#include "UniformDielectric.hpp"
46+
#include "SphericalDiffuse.hpp"
4847
#include "TestingMolecules.hpp"
48+
#include "UniformDielectric.hpp"
4949
#include "Vacuum.hpp"
5050

5151
struct CollocationIntegratorTest {
@@ -70,7 +70,7 @@ struct CollocationIntegratorTest {
7070
};
7171

7272
/*! \class CollocationIntegrator
73-
* \test \b CollocationIntegratorTest_vacuum tests the numerical evaluation of the vacuum onal elements of S and D
73+
* \test \b CollocationIntegratorTest_vacuum tests the numerical evaluation of the vacuum diagonal elements of S and D
7474
*/
7575
BOOST_FIXTURE_TEST_CASE(vacuum, CollocationIntegratorTest)
7676
{
@@ -79,7 +79,7 @@ BOOST_FIXTURE_TEST_CASE(vacuum, CollocationIntegratorTest)
7979
BOOST_TEST_MESSAGE("Vacuum");
8080
Eigen::VectorXd S_results = Eigen::VectorXd::Zero(cavity.size());
8181
for (int i = 0; i < cavity.size(); ++i) {
82-
S_results(i) = gf.onalS(cavity.elements(i));
82+
S_results(i) = gf.diagonalS(cavity.elements(i));
8383
}
8484
// In case you need to update the reference files...
8585
/*
@@ -94,15 +94,15 @@ BOOST_FIXTURE_TEST_CASE(vacuum, CollocationIntegratorTest)
9494
for (int i = 0; i < cavity.size(); ++i) {
9595
BOOST_REQUIRE_CLOSE(S_reference(i), S_results(i), 1.0e-12);
9696
}
97-
BOOST_TEST_MESSAGE("S operator onal by collocation");
97+
BOOST_TEST_MESSAGE("S operator diagonal by collocation");
9898
for (int i = 0; i < cavity.size(); ++i) {
9999
BOOST_TEST_MESSAGE("S_{" << i+1 << ", " << i+1 << "} = "
100100
<< std::setprecision(std::numeric_limits<long double>::digits10) << S_results(i));
101101
}
102102

103103
Eigen::VectorXd D_results = Eigen::VectorXd::Zero(cavity.size());
104104
for (int i = 0; i < cavity.size(); ++i) {
105-
D_results(i) = gf.onalD(cavity.elements(i));
105+
D_results(i) = gf.diagonalD(cavity.elements(i));
106106
}
107107
// In case you need to update the reference files...
108108
/*
@@ -115,15 +115,15 @@ BOOST_FIXTURE_TEST_CASE(vacuum, CollocationIntegratorTest)
115115
for (int i = 0; i < cavity.size(); ++i) {
116116
BOOST_REQUIRE_CLOSE(D_reference(i), D_results(i), 1.0e-12);
117117
}
118-
BOOST_TEST_MESSAGE("D operator onal by collocation");
118+
BOOST_TEST_MESSAGE("D operator diagonal by collocation");
119119
for (int i = 0; i < cavity.size(); ++i) {
120120
BOOST_TEST_MESSAGE("D_{" << i+1 << ", " << i+1 << "} = "
121121
<< std::setprecision(std::numeric_limits<long double>::digits10) << D_results(i));
122122
}
123123
}
124124

125125
/*! \class CollocationIntegrator
126-
* \test \b CollocationIntegratorTest_uniformdielectric tests the numerical evaluation of the uniform dielectric onal elements of S and D
126+
* \test \b CollocationIntegratorTest_uniformdielectric tests the numerical evaluation of the uniform dielectric diagonal elements of S and D
127127
*/
128128
BOOST_FIXTURE_TEST_CASE(uniformdielectric, CollocationIntegratorTest)
129129
{
@@ -132,7 +132,7 @@ BOOST_FIXTURE_TEST_CASE(uniformdielectric, CollocationIntegratorTest)
132132
BOOST_TEST_MESSAGE("UniformDielectric");
133133
Eigen::VectorXd S_results = Eigen::VectorXd::Zero(cavity.size());
134134
for (int i = 0; i < cavity.size(); ++i) {
135-
S_results(i) = gf.onalS(cavity.elements(i));
135+
S_results(i) = gf.diagonalS(cavity.elements(i));
136136
}
137137
// In case you need to update the reference files...
138138
/*
@@ -147,15 +147,15 @@ BOOST_FIXTURE_TEST_CASE(uniformdielectric, CollocationIntegratorTest)
147147
for (int i = 0; i < cavity.size(); ++i) {
148148
BOOST_REQUIRE_CLOSE(S_reference(i), S_results(i), 1.0e-12);
149149
}
150-
BOOST_TEST_MESSAGE("S operator onal by collocation");
150+
BOOST_TEST_MESSAGE("S operator diagonal by collocation");
151151
for (int i = 0; i < cavity.size(); ++i) {
152152
BOOST_TEST_MESSAGE("S_{" << i+1 << ", " << i+1 << "} = "
153153
<< std::setprecision(std::numeric_limits<long double>::digits10) << S_results(i));
154154
}
155155

156156
Eigen::VectorXd D_results = Eigen::VectorXd::Zero(cavity.size());
157157
for (int i = 0; i < cavity.size(); ++i) {
158-
D_results(i) = gf.onalD(cavity.elements(i));
158+
D_results(i) = gf.diagonalD(cavity.elements(i));
159159
}
160160
// In case you need to update the reference files...
161161
/*
@@ -168,7 +168,7 @@ BOOST_FIXTURE_TEST_CASE(uniformdielectric, CollocationIntegratorTest)
168168
for (int i = 0; i < cavity.size(); ++i) {
169169
BOOST_REQUIRE_CLOSE(D_reference(i), D_results(i), 1.0e-12);
170170
}
171-
BOOST_TEST_MESSAGE("D operator onal by collocation");
171+
BOOST_TEST_MESSAGE("D operator diagonal by collocation");
172172
for (int i = 0; i < cavity.size(); ++i) {
173173
BOOST_TEST_MESSAGE("D_{" << i+1 << ", " << i+1 << "} = "
174174
<< std::setprecision(std::numeric_limits<long double>::digits10) << D_results(i));
@@ -179,12 +179,12 @@ BOOST_FIXTURE_TEST_CASE(tanhsphericaldiffuse, CollocationIntegratorTest)
179179
{
180180
double width = 5.0;
181181
double sphereRadius = 100.0;
182-
TanhSphericalDiffuse gf(epsilon, epsilon, width, sphereRadius, Eigen::Vector3d::Zero());
182+
SphericalDiffuse<CollocationIntegrator<Numerical, TanhDiffuse>, TanhDiffuse> gf(epsilon, epsilon, width, sphereRadius, Eigen::Vector3d::Zero());
183183

184184
BOOST_TEST_MESSAGE("TanhSphericalDiffuse");
185185
Eigen::VectorXd S_results = Eigen::VectorXd::Zero(cavity.size());
186186
for (int i = 0; i < cavity.size(); ++i) {
187-
S_results(i) = gf.onalS(cavity.elements(i));
187+
S_results(i) = gf.diagonalS(cavity.elements(i));
188188
}
189189
// In case you need to update the reference files...
190190
/*
@@ -199,15 +199,15 @@ BOOST_FIXTURE_TEST_CASE(tanhsphericaldiffuse, CollocationIntegratorTest)
199199
for (int i = 0; i < cavity.size(); ++i) {
200200
BOOST_CHECK_CLOSE(S_reference(i), S_results(i), 1.0e-08);
201201
}
202-
BOOST_TEST_MESSAGE("S operator onal by collocation");
202+
BOOST_TEST_MESSAGE("S operator diagonal by collocation");
203203
for (int i = 0; i < cavity.size(); ++i) {
204204
BOOST_TEST_MESSAGE("S_{" << i+1 << ", " << i+1 << "} = "
205205
<< std::setprecision(std::numeric_limits<long double>::digits10) << S_results(i));
206206
}
207207

208208
Eigen::VectorXd D_results = Eigen::VectorXd::Zero(cavity.size());
209209
for (int i = 0; i < cavity.size(); ++i) {
210-
D_results(i) = gf.onalD(cavity.elements(i));
210+
D_results(i) = gf.diagonalD(cavity.elements(i));
211211
}
212212
// In case you need to update the reference files...
213213
/*
@@ -220,7 +220,7 @@ BOOST_FIXTURE_TEST_CASE(tanhsphericaldiffuse, CollocationIntegratorTest)
220220
for (int i = 0; i < cavity.size(); ++i) {
221221
BOOST_CHECK_CLOSE(D_reference(i), D_results(i), 1.0e-06);
222222
}
223-
BOOST_TEST_MESSAGE("D operator onal by collocation");
223+
BOOST_TEST_MESSAGE("D operator diagonal by collocation");
224224
for (int i = 0; i < cavity.size(); ++i) {
225225
BOOST_TEST_MESSAGE("D_{" << i+1 << ", " << i+1 << "} = "
226226
<< std::setprecision(std::numeric_limits<long double>::digits10) << D_results(i));

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