Skip to content

L
libcifpp
Commit efd96f18 by maarten
Options

dict optie in stats 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@296 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent deeac050
Showing with 87 additions and 81 deletions
src/AtomShape.cpp
...@@ -15,12 +15,12 @@ namespace mmcif ...@@ -15,12 +15,12 @@ namespace mmcif
template <class F> template <class F>
NewuoaClosure make_closure(F &function) { NewuoaClosure make_closure(F &function) {
struct Wrap { struct Wrap {
static double call(void *data, long n, const double *values) { static double call(void *data, long n, const double *values) {
return reinterpret_cast<F *>(data)->operator()(n, values); return reinterpret_cast<F *>(data)->operator()(n, values);
} }
}; };
return NewuoaClosure {&function, &Wrap::call}; return NewuoaClosure {&function, &Wrap::call};
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -67,7 +67,7 @@ double sineIntegration(double x) ...@@ -67,7 +67,7 @@ double sineIntegration(double x)
const P const P
kF[] = kF[] =
{ {
{ 1, 1, }, { 1, 1, },
{ 7.44437068161936700618e2, 7.46437068161927678031e2, }, { 7.44437068161936700618e2, 7.46437068161927678031e2, },
{ 1.96396372895146869801e5, 1.97865247031583951450e5, }, { 1.96396372895146869801e5, 1.97865247031583951450e5, },
{ 2.37750310125431834034e7, 2.41535670165126845144e7, }, { 2.37750310125431834034e7, 2.41535670165126845144e7, },
...@@ -77,20 +77,20 @@ double sineIntegration(double x) ...@@ -77,20 +77,20 @@ double sineIntegration(double x)
{ 4.20968180571076940208e12, 5.06084464593475076774e12, }, { 4.20968180571076940208e12, 5.06084464593475076774e12, },
{ 1.00795182980368574617e13, 1.43468549171581016479e13, }, { 1.00795182980368574617e13, 1.43468549171581016479e13, },
{ 4.94816688199951963482e12, 1.11535493509914254097e13, }, { 4.94816688199951963482e12, 1.11535493509914254097e13, },
{ -4.94701168645415959931e11, 0 } { -4.94701168645415959931e11, 0 }
}, },
kG[] = { kG[] = {
{ 1, 1, }, { 1, 1, },
{ 8.1359520115168615e2, 8.19595201151451564e2, }, { 8.1359520115168615e2, 8.19595201151451564e2, },
{ 2.35239181626478200e5, 2.40036752835578777e5, }, { 2.35239181626478200e5, 2.40036752835578777e5, },
{ 3.12557570795778731e7, 3.26026661647090822e7, }, { 3.12557570795778731e7, 3.26026661647090822e7, },
{ 2.06297595146763354e9, 2.23355543278099360e9, }, { 2.06297595146763354e9, 2.23355543278099360e9, },
{ 6.83052205423625007e10, 7.87465017341829930e10, }, { 6.83052205423625007e10, 7.87465017341829930e10, },
{ 1.09049528450362786e12, 1.39866710696414565e12, }, { 1.09049528450362786e12, 1.39866710696414565e12, },
{ 7.57664583257834349e12, 1.17164723371736605e13, }, { 7.57664583257834349e12, 1.17164723371736605e13, },
{ 1.81004487464664575e13, 4.01839087307656620e13, }, { 1.81004487464664575e13, 4.01839087307656620e13, },
{ 6.43291613143049485e12, 3.99653257887490811e13, }, { 6.43291613143049485e12, 3.99653257887490811e13, },
{ -1.36517137670871689e12, 0 } { -1.36517137670871689e12, 0 }
}; };
double xs = pow(x, -2); double xs = pow(x, -2);
...@@ -257,69 +257,69 @@ double DensityIntegration::integrateRadius(float perc, float occupancy, double y ...@@ -257,69 +257,69 @@ double DensityIntegration::integrateRadius(float perc, float occupancy, double y
// code from newuoa-example // code from newuoa-example
const long variables_count = 1; const long variables_count = 1;
const long number_of_interpolation_conditions = (variables_count + 1)*(variables_count + 2)/2; const long number_of_interpolation_conditions = (variables_count + 1)*(variables_count + 2)/2;
double variables_values[] = { initialValue }; double variables_values[] = { initialValue };
const double initial_trust_region_radius = 1e-3; const double initial_trust_region_radius = 1e-3;
const double final_trust_region_radius = 1e3; const double final_trust_region_radius = 1e3;
const long max_function_calls_count = 100; const long max_function_calls_count = 100;
const size_t working_space_size = NEWUOA_WORKING_SPACE_SIZE(variables_count, const size_t working_space_size = NEWUOA_WORKING_SPACE_SIZE(variables_count,
number_of_interpolation_conditions); number_of_interpolation_conditions);
double working_space[working_space_size]; double working_space[working_space_size];
auto function = [&] (long n, const double *x) auto function = [&] (long n, const double *x)
{ {
assert(n == 1); assert(n == 1);
return this->integrateDensity(x[0], -1, fst); return this->integrateDensity(x[0], -1, fst);
}; };
auto closure = make_closure(function); auto closure = make_closure(function);
double result = newuoa_closure( double result = newuoa_closure(
&closure, &closure,
variables_count, variables_count,
number_of_interpolation_conditions, number_of_interpolation_conditions,
variables_values, variables_values,
initial_trust_region_radius, initial_trust_region_radius,
final_trust_region_radius, final_trust_region_radius,
max_function_calls_count, max_function_calls_count,
working_space); working_space);
// //
const double kRE = 5e-5; const double kRE = 5e-5;
double y1 = 0; double y1 = 0;
double y2 = -result; double y2 = -result;
double x1 = 0; double x1 = 0;
double x2 = variables_values[0]; double x2 = variables_values[0];
if (y2 > yt) if (y2 > yt)
{ {
for (int it = 0; it < 100; ++it) for (int it = 0; it < 100; ++it)
{ {
double x = 0.5 * (x1 + x2); double x = 0.5 * (x1 + x2);
double y = integrateDensity(x, 1, fst); double y = integrateDensity(x, 1, fst);
if (abs(y - yt) < kRE * abs(yt)) if (abs(y - yt) < kRE * abs(yt))
{ {
result = x; result = x;
break; break;
} }
if ((y1 < yt and y < yt) or (y1 > yt and y > yt)) if ((y1 < yt and y < yt) or (y1 > yt and y > yt))
{ {
x1 = x; x1 = x;
y1 = y; y1 = y;
} }
else else
{ {
x2 = x; x2 = x;
y2 = y; y2 = y;
} }
} }
} }
else else
result = x2; result = x2;
return result; return result;
} }
...@@ -386,7 +386,7 @@ struct AtomShapeImpl ...@@ -386,7 +386,7 @@ struct AtomShapeImpl
float integratedRadius(float perc) const float integratedRadius(float perc) const
{ {
return mIntegrator.integrateRadius(perc, mOccupancy, mYi, mFst); return mIntegrator.integrateRadius(perc, mOccupancy, mYi, mFst);
} }
float calculatedDensity(float r) const float calculatedDensity(float r) const
......
src/Cif++.cpp
...@@ -7,6 +7,7 @@ ...@@ -7,6 +7,7 @@
#include <regex> #include <regex>
#include <set> #include <set>
#include <unordered_map> #include <unordered_map>
#include <numeric>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
#include <boost/filesystem/operations.hpp> #include <boost/filesystem/operations.hpp>
......
src/Compound.cpp
...@@ -3,6 +3,7 @@ ...@@ -3,6 +3,7 @@
#include "cif++/Config.h" #include "cif++/Config.h"
#include <map> #include <map>
#include <numeric>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
#include <boost/filesystem/operations.hpp> #include <boost/filesystem/operations.hpp>
......
src/Edia.cpp
...@@ -2,6 +2,8 @@ ...@@ -2,6 +2,8 @@
#include "cif++/Config.h" #include "cif++/Config.h"
#include <numeric>
#include <boost/format.hpp> #include <boost/format.hpp>
#include "cif++/mrsrc.h" #include "cif++/mrsrc.h"
......
src/Secondary.cpp
...@@ -7,6 +7,8 @@ ...@@ -7,6 +7,8 @@
#include "cif++/Config.h" #include "cif++/Config.h"
#include <numeric>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
#include "cif++/Structure.h" #include "cif++/Structure.h"
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment