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openbabel/test/unitcell.cpp
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/**********************************************************************
Copyright (C) 2003-2005 by Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/math/matrix3x3.h>
#include <openbabel/obutil.h>
#include <openbabel/generic.h>
#include <cstdlib>
using namespace std;
using namespace OpenBabel;
#ifdef TESTDATADIR
string ptestdatadir = TESTDATADIR;
string punitcell_file = ptestdatadir + "unitcell.txt";
string presults_file = ptestdatadir + "unitcell_results.txt";
#else
string punitcell_file = "files/unitcell.txt";
string presults_file = "files/unitcell_results.txt";
#endif
int unitcell(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
cout << "# Testing unit cell transformations ..." << endl;
cout << "1..12" << endl;
double a, b, c, alpha, beta, gamma;
vector3 v1, v2, v3, v4, v5, v6, v7, v8, v9;
vector3 coords1, coords2, tmpcoords;
double x = 0.0, y = 0.0, z = 0.0;
char buffer[BUFF_SIZE];
std::ifstream ifs, results;
OBUnitCell cell, cell2;
vector<vector3> v3Return;
vector<string> vs;
unsigned int currTest = 1;
if (!SafeOpen(ifs, punitcell_file.c_str()))
{
cout << "Bail out! Couldn't open test file 'unitcell.txt'" << endl;
return(-1);
}
if (!SafeOpen(results, presults_file.c_str()))
{
cout << "Bail out! Couldn't open test file 'unitcell_results.txt'" << endl;
return(-1);
}
// Get cell vectors
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%lf %lf %lf",&x, &y, &z);
v1.Set(x, y, z);
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%lf %lf %lf",&x, &y, &z);
v2.Set(x, y, z);
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%lf %lf %lf",&x, &y, &z);
v3.Set(x, y, z);
cell.SetData(v1, v2, v3);
// Get test coordinates
ifs.getline(buffer,BUFF_SIZE); // blank
// Cartesian, outside of uc
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%lf %lf %lf",&x, &y, &z);
coords1.Set(x, y, z);
// Fractional, outside of uc
ifs.getline(buffer,BUFF_SIZE);
sscanf(buffer,"%lf %lf %lf",&x, &y, &z);
coords2.Set(x, y, z);
// Test
a = cell.GetA();
b = cell.GetB();
c = cell.GetC();
alpha = cell.GetAlpha();
beta = cell.GetBeta();
gamma = cell.GetGamma();
results.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (vs.size() != 6)
{
cout << "Bail out! Cannot parse results file 'unitcell_results.txt'"
<< endl;
return(-1);
}
if ( IsNear(a, atof(vs[0].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # a distance" << endl;
else
cout << "not ok " << currTest++ << " # a distance" << endl;
if ( IsNear(b, atof(vs[1].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # b distance" << endl;
else
cout << "not ok " << currTest++ << " # b distance" << endl;
if ( IsNear(c, atof(vs[2].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # c distance" << endl;
else
cout << "not ok " << currTest++ << " # c distance" << endl;
if ( IsNear(alpha, atof(vs[3].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # alpha angle" << endl;
else
cout << "not ok " << currTest++ << " # alpha angle" << alpha << endl;
if ( IsNear(beta, atof(vs[4].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # beta angle" << endl;
else
cout << "not ok " << currTest++ << " # beta angle " << beta << endl;
if ( IsNear(gamma, atof(vs[5].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # gamma angle" << endl;
else
cout << "not ok " << currTest++ << " # gamma angle: " << gamma << endl;
// check to see if vector and a,b,c methods are equivalent
cell2.SetData(a, b, c, alpha, beta, gamma);
if ( IsNear(a, cell2.GetA(), 1.0e-3) )
cout << "ok " << currTest++ << " # a distance" << endl;
else
cout << "not ok " << currTest++ << " # a distance" << endl;
if ( IsNear(b, cell2.GetB(), 1.0e-3) )
cout << "ok " << currTest++ << " # b distance" << endl;
else
cout << "not ok " << currTest++ << " # b distance" << endl;
if ( IsNear(c, cell2.GetC(), 1.0e-3) )
cout << "ok " << currTest++ << " # c distance" << endl;
else
cout << "not ok " << currTest++ << " # c distance" << endl;
if ( IsNear(alpha, cell2.GetAlpha(), 1.0e-3) )
cout << "ok " << currTest++ << " # a angle" << endl;
else
cout << "not ok " << currTest++ << " # a angle" << endl;
if ( IsNear(beta, cell2.GetBeta(), 1.0e-3) )
cout << "ok " << currTest++ << " # beta angle" << endl;
else
cout << "not ok " << currTest++ << " # beta angle" << endl;
if ( IsNear(gamma, cell2.GetGamma(), 1.0e-3) )
cout << "ok " << currTest++ << " # gamma angle" << endl;
else
cout << "not ok " << currTest++ << " # gamma angle" << endl;
v3Return = cell2.GetCellVectors();
v4 = v3Return[0];
// cout << v4 << endl;
v5 = v3Return[1];
// cout << v5 << endl;
v6 = v3Return[2];
// cout << v6 << endl;
v9 = vector3(1.0f, 1.0f, 1.0f);
v9 = cell2.FractionalToCartesian(v9);
// cout << v9 << endl;
cout << "# Testing unit cell coordinate functions ..." << endl;
cout << "13..24" << endl;
// Cartesian wrapping
results.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (vs.size() != 3)
{
cout << "Bail out! Cannot parse results file 'unitcell_results.txt'"
<< endl;
return(-1);
}
tmpcoords = cell2.WrapCartesianCoordinate(coords1);
// cout << "Wrapped cartesian : " << tmpcoords << endl;
if ( IsNear(tmpcoords[0], atof(vs[0].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped cartesian x" << endl;
else
cout << "not ok " << currTest++ << " # wrapped cartesian x" << endl;
if ( IsNear(tmpcoords[1], atof(vs[1].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped cartesian y" << endl;
else
cout << "not ok " << currTest++ << " # wrapped cartesian y" << endl;
if ( IsNear(tmpcoords[2], atof(vs[2].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped cartesian z" << endl;
else
cout << "not ok " << currTest++ << " # wrapped cartesian z" << endl;
// Fractional wrapping
results.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (vs.size() != 3)
{
cout << "Bail out! Cannot parse results file 'unitcell_results.txt'"
<< endl;
return(-1);
}
tmpcoords = cell2.WrapFractionalCoordinate(coords2);
// cout << "Wrapped fractional: " << tmpcoords << endl;
if ( IsNear(tmpcoords[0], atof(vs[0].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped fractional x" << endl;
else
cout << "not ok " << currTest++ << " # wrapped fractional x" << endl;
if ( IsNear(tmpcoords[1], atof(vs[1].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped fractional y" << endl;
else
cout << "not ok " << currTest++ << " # wrapped fractional y" << endl;
if ( IsNear(tmpcoords[2], atof(vs[2].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # wrapped fractional z" << endl;
else
cout << "not ok " << currTest++ << " # wrapped fractional z" << endl;
// cart2frac
results.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (vs.size() != 3)
{
cout << "Bail out! Cannot parse results file 'unitcell_results.txt'"
<< endl;
return(-1);
}
tmpcoords = cell2.CartesianToFractional(coords1);
// cout << "cart2frac: " << tmpcoords << endl;
if ( IsNear(tmpcoords[0], atof(vs[0].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # cart2frac x" << endl;
else
cout << "not ok " << currTest++ << " # cart2frac x" << endl;
if ( IsNear(tmpcoords[1], atof(vs[1].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # cart2frac y" << endl;
else
cout << "not ok " << currTest++ << " # cart2frac y" << endl;
if ( IsNear(tmpcoords[2], atof(vs[2].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # cart2frac z" << endl;
else
cout << "not ok " << currTest++ << " # cart2frac z" << endl;
// frac2cart
results.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
if (vs.size() != 3)
{
cout << "Bail out! Cannot parse results file 'unitcell_results.txt'"
<< endl;
return(-1);
}
tmpcoords = cell2.FractionalToCartesian(coords1);
// cout << "frac2cart: " << tmpcoords << endl;
if ( IsNear(tmpcoords[0], atof(vs[0].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # frac2cart x" << endl;
else
cout << "not ok " << currTest++ << " # frac2cart x" << endl;
if ( IsNear(tmpcoords[1], atof(vs[1].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # frac2cart y" << endl;
else
cout << "not ok " << currTest++ << " # frac2cart y" << endl;
if ( IsNear(tmpcoords[2], atof(vs[2].c_str()), 1.0e-3) )
cout << "ok " << currTest++ << " # frac2cart z" << endl;
else
cout << "not ok " << currTest++ << " # frac2cart z" << endl;
cout << "# cell volume " << cell.GetCellVolume() << endl;
cout << "# lattice type " << cell.GetLatticeType() << endl;
cout << "# cell volume " << cell2.GetCellVolume() << endl;
cout << "# lattice type " << cell2.GetLatticeType() << endl;
return(0); // success
}
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