/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/oenv.h"
#include "gromacs/utility/smalloc.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"
#include "testutils/testfilemanager.h"
-//! Number of data files for testing.
-#define expTestNrTypes 3
-
namespace gmx
{
namespace
{
+class ExpfitData
+{
+ public:
+ int nrLines_;
+ std::vector<real> x_, y_;
+ real startTime_, endTime_, dt_;
+};
+
class ExpfitTest : public ::testing::Test
{
protected:
- static int nrLines_;
- static std::vector<real> values_[expTestNrTypes];
- static int nrColumns_;
- static std::vector<real> standardDev_;
- static real startTime_;
- static real endTime_;
- static real timeDeriv_;
- test::TestReferenceData refData_;
- test::TestReferenceChecker checker_;
+ static std::vector<ExpfitData> data_;
+ test::TestReferenceData refData_;
+ test::TestReferenceChecker checker_;
ExpfitTest( )
: checker_(refData_.rootChecker())
{
// Static initiation, only run once every test.
static void SetUpTestCase()
{
- double ** tempValues;
- std::string fileName[expTestNrTypes];
- fileName[0] = test::TestFileManager::getInputFilePath("testINVEXP.xvg");
- fileName[1] = test::TestFileManager::getInputFilePath("testPRES.xvg");
- fileName[2] = test::TestFileManager::getInputFilePath("testEXP.xvg");
- for (int i = 0; i < expTestNrTypes; i++)
+ double ** tempValues = NULL;
+ std::vector<std::string> fileName;
+ fileName.push_back(test::TestFileManager::getInputFilePath("testINVEXP.xvg"));
+ fileName.push_back(test::TestFileManager::getInputFilePath("testPRES.xvg"));
+ fileName.push_back(test::TestFileManager::getInputFilePath("testINVEXP79.xvg"));
+ fileName.push_back(test::TestFileManager::getInputFilePath("testERF.xvg"));
+ fileName.push_back(test::TestFileManager::getInputFilePath("testERREST.xvg"));
+ for (std::vector<std::string>::iterator i = fileName.begin(); i < fileName.end(); ++i)
{
- const char * name = fileName[i].c_str();
- // TODO: this assumes all files have the same length.
- nrLines_ = read_xvg(name, &tempValues, &nrColumns_);
-
- // Generating standard deviation
- if (i == 0)
+ const char * name = i->c_str();
+ int nrColumns;
+ ExpfitData ed;
+ ed.nrLines_ = read_xvg(name, &tempValues, &nrColumns);
+ ed.dt_ = tempValues[0][1] - tempValues[0][0];
+ ed.startTime_ = tempValues[0][0];
+ ed.endTime_ = tempValues[0][ed.nrLines_-1];
+ for (int j = 0; j < ed.nrLines_; j++)
{
- double fac = 1.0/nrLines_;
- for (int j = 0; j < nrLines_; j++)
- {
- standardDev_.push_back(fac);
- }
- timeDeriv_ = tempValues[0][1] - tempValues[0][0];
- startTime_ = tempValues[0][0];
- endTime_ = tempValues[0][nrLines_-1];
- }
-
- for (int j = 0; j < nrLines_; j++)
- {
- values_[i].push_back((real)tempValues[1][j]);
+ ed.x_.push_back((real)tempValues[0][j]);
+ ed.y_.push_back((real)tempValues[1][j]);
}
+ data_.push_back(ed);
// Free memory that was allocated in read_xvg
- for (int i = 0; i < nrColumns_; i++)
+ for (int j = 0; j < nrColumns; j++)
{
- sfree(tempValues[i]);
- tempValues[i] = NULL;
+ sfree(tempValues[j]);
+ tempValues[j] = NULL;
}
sfree(tempValues);
tempValues = NULL;
{
}
- void test(int type, double result[], double tolerance, int testType)
+ void test(int type, double result[], double tolerance,
+ unsigned int testType)
{
- int nfitparm = effnNparams(type);
-
- do_lmfit(nrLines_, &values_[testType][0], &standardDev_[0], timeDeriv_,
- NULL, startTime_, endTime_, NULL, false, type, result, 0);
+ int nfitparm = effnNparams(type);
+ output_env_t oenv;
+ if (testType >= data_.size())
+ {
+ GMX_THROW(InvalidInputError("testType out of range"));
+ }
+ output_env_init_default(&oenv);
+ do_lmfit(data_[testType].nrLines_,
+ &(data_[testType].y_[0]),
+ NULL,
+ data_[testType].dt_,
+ &(data_[testType].x_[0]),
+ data_[testType].startTime_,
+ data_[testType].endTime_,
+ oenv, false, type, result, 0, NULL);
+ output_env_done(oenv);
checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, tolerance));
checker_.checkSequenceArray(nfitparm, result, "result");
}
//static var
-int ExpfitTest::nrLines_;
-//cppcheck-suppress arrayIndexOutOfBounds fixed in 1.68-dev
-std::vector<real> ExpfitTest::values_[expTestNrTypes];
-int ExpfitTest::nrColumns_;
-std::vector<real> ExpfitTest::standardDev_;
-real ExpfitTest::startTime_;
-real ExpfitTest::endTime_;
-real ExpfitTest::timeDeriv_;
+std::vector<ExpfitData> ExpfitTest::data_;
TEST_F (ExpfitTest, EffnEXP1) {
double param[] = {25};
- test(effnEXP1, param, 1e-6, 0);
+ test(effnEXP1, param, 1e-5, 0);
}
TEST_F (ExpfitTest, EffnEXP2) {
double param[] = {35, 0.5};
- test(effnEXP2, param, 1e-6, 0);
+ test(effnEXP2, param, 3e-5, 0);
}
-TEST_F (ExpfitTest, EffnEXP3) {
- double param[] = {45, 0.5, 5};
- test(effnEXP3, param, 1e-4, 0);
+TEST_F (ExpfitTest, EffnEXPEXP) {
+ double param[] = {5, 0.5, 45};
+ test(effnEXPEXP, param, 1e-2, 0);
}
TEST_F (ExpfitTest, EffnEXP5) {
double param[] = {0.5, 5, 0.5, 50, 0.002};
- test(effnEXP5, param, 1e-4, 0);
+ test(effnEXP5, param, 1e-2, 2);
}
TEST_F (ExpfitTest, EffnEXP7) {
- double param[] = {0.5, 5, -0.02, 0.5, 0.5, 50, -0.002};
- test(effnEXP7, param, 1e-4, 0);
+ double param[] = {0.1, 2, 0.5, 30, 0.3, 50, -0.002};
+ test(effnEXP7, param, 1e-2, 2);
}
TEST_F (ExpfitTest, EffnEXP9) {
- double param[] = {2, 1200, -1, 300, 0.7, 70, 0.5, 6, -0.5};
- test(effnEXP9, param, 4e-2, 0);
+ double param[] = {0.4, 5, 0.2, 30, 0.1, 70, 0.2, 200, -0.05};
+ test(effnEXP9, param, 4e-2, 2);
}
TEST_F (ExpfitTest, EffnERF) {
- double param[] = {0.5, 0.5, 0.5, 1};
- test(effnERF, param, 1e-2, 0);
+ double param[] = {80, 120, 180, 5};
+ test(effnERF, param, 1e-1, 3);
}
TEST_F (ExpfitTest, EffnERREST) {
- double param[] = {0.5, 0.7, 0.3};
- test(effnERREST, param, 1e-4, 2);
+ double param[] = {1, 0.9, 100};
+ test(effnERREST, param, 5e-3, 4);
}
TEST_F (ExpfitTest, EffnVAC) {
- double param[] = {0.5, 0.05};
- test(effnVAC, param, 1e-4, 0);
+ double param[] = {30, 0.0};
+ test(effnVAC, param, 0.05, 0);
}
-TEST_F (ExpfitTest, DISABLED_EffnPRES) {
- //TODO: This test is prodocues NaNs and INFs. Fix and then reactivate.
- double param[] = {0, 10, 4, 1, 0.5, 1};
+TEST_F (ExpfitTest, EffnPRES) {
+ double param[] = {0.6, 10, 7, 1, 0.25, 2};
test(effnPRES, param, 1e-4, 1);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff