* Empty if the free energy output has not been requested.
*/
std::vector<real> dgsFactor_;
+ //! Calculation algorithm.
+ SurfaceAreaCalculator calculator_;
// Copy and assign disallowed by base.
};
}
}
+ calculator_.setDotCount(ndots_);
+
// Initialize all the output data objects and initialize the output plotters.
area_.setColumnCount(0, 1 + outputSel_.size());
real totarea, totvolume;
real *area = NULL, *surfacedots = NULL;
int nsurfacedots;
- int retval = nsc_dclm_pbc(surfaceSel.coordinates().data(), &radii_[0],
- frameData.index_.size(), ndots_, flag, &totarea,
- &area, &totvolume, &surfacedots, &nsurfacedots,
- &frameData.index_[0],
- pbc != NULL ? pbc->ePBC : epbcNONE,
- pbc != NULL ? pbc->box : NULL);
+ calculator_.calculate(surfaceSel.coordinates().data(), &radii_[0], pbc,
+ frameData.index_.size(), &frameData.index_[0], flag,
+ &totarea, &totvolume, &area,
+ &surfacedots, &nsurfacedots);
// Unpack the atomwise areas into the frameData.atomAreas_ array for easier
// indexing in the case of dynamic surfaceSel.
if (area != NULL)
sfree(area);
}
scoped_guard_sfree dotsGuard(surfacedots);
- if (retval != 0)
- {
- GMX_THROW(InternalError("nsc_dclm_pbc failed"));
- }
if (bConnolly)
{
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#define TEST_NSC 0
-
-#define TEST_ARC 0
-#define TEST_DOD 0
-#define TEST_CUBE 0
-
#define UNSP_ICO_DOD 9
#define UNSP_ICO_ARC 10
-real *xpunsp = NULL;
-real del_cube;
-int n_dot, ico_cube, last_n_dot = 0, last_densit = 0, last_unsp = 0;
-int last_cubus = 0;
+static real *xpunsp = NULL;
+static real del_cube;
+static int n_dot, ico_cube, last_n_dot = 0, last_densit = 0, last_unsp = 0;
+static int last_cubus = 0;
#define FOURPI (4.*M_PI)
#define TORAD(A) ((A)*0.017453293)
#define DP_TOL 0.001
#define UPDATE_FL __file__ = __FILE__, __line__ = __LINE__
-const char * __file__; /* declared versions of macros */
-int __line__; /* __FILE__ and __LINE__ */
+static const char * __file__; /* declared versions of macros */
+static int __line__; /* __FILE__ and __LINE__ */
#ifdef ERROR
#undef ERROR
#endif
#define ERROR UPDATE_FL, error
-void error(const char *fmt, ...)
+static void error(const char *fmt, ...)
{
va_list args;
fprintf(stderr,
fprintf(stderr, "\n---> Execution stopped !\n\n");
}
-#define WARNING UPDATE_FL, warning2
-void warning2(const char *fmt, ...)
-{
- va_list args;
- fprintf(stderr,
- "\n---> WARNING : line %i in file %s\n",
- __line__, __file__);
- va_start(args, fmt);
- vfprintf(stderr, fmt, args);
- va_end(args);
- fprintf(stderr, " ...!\n\n");
- fflush(stderr);
- fflush(stdout);
-}
-
#define ASIN safe_asin
-real safe_asin(real f)
+static real safe_asin(real f)
{
if ( (fabs(f) < 1.00) )
{
return(M_PI_2);
}
-
-
-
/* routines for dot distributions on the surface of the unit sphere */
-real rg, rh;
+static real rh;
-void icosaeder_vertices(real *xus)
+static void icosaeder_vertices(real *xus)
{
rh = sqrt(1.-2.*cos(TORAD(72.)))/(1.-cos(TORAD(72.)));
- rg = cos(TORAD(72.))/(1.-cos(TORAD(72.)));
+ const real rg = cos(TORAD(72.))/(1.-cos(TORAD(72.)));
/* icosaeder vertices */
xus[ 0] = 0.; xus[ 1] = 0.; xus[ 2] = 1.;
xus[ 3] = rh*cos(TORAD(72.)); xus[ 4] = rh*sin(TORAD(72.)); xus[ 5] = rg;
}
-void divarc(real x1, real y1, real z1,
- real x2, real y2, real z2,
- int div1, int div2, real *xr, real *yr, real *zr)
+static void divarc(real x1, real y1, real z1,
+ real x2, real y2, real z2,
+ int div1, int div2, real *xr, real *yr, real *zr)
{
real xd, yd, zd, dd, d1, d2, s, x, y, z;
*xr = x/dd; *yr = y/dd; *zr = z/dd;
}
-int ico_dot_arc(int densit) /* densit...required dots per unit sphere */
+static int ico_dot_arc(int densit) /* densit...required dots per unit sphere */
{
/* dot distribution on a unit sphere based on an icosaeder *
* great circle average refining of icosahedral face */
} /* end of if (tess > 1) */
return n_dot;
-} /* end of routine ico_dot_arc */
+} /* end of routine ico_dot_arc */
-int ico_dot_dod(int densit) /* densit...required dots per unit sphere */
+static int ico_dot_dod(int densit) /* densit...required dots per unit sphere */
{
/* dot distribution on a unit sphere based on an icosaeder *
* great circle average refining of icosahedral face */
return n_dot;
} /* end of routine ico_dot_dod */
-int unsp_type(int densit)
+static int unsp_type(int densit)
{
int i1, i2;
i1 = 1;
}
}
-int make_unsp(int densit, int mode, int * num_dot, int cubus)
+static void make_unsp(int densit, int mode, int * num_dot, int cubus)
{
int *ico_wk, *ico_pt;
- int ndot, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
+ int ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
real *xus;
int *work;
real x, y, z;
free(xpunsp);
}
- k = 1; if (mode < 0)
+ k = 1;
+ if (mode < 0)
{
- k = 0; mode = -mode;
+ k = 0;
+ mode = -mode;
}
+ // Assignment to satisfy cppcheck.
+ int ndot = 0;
if (mode == UNSP_ICO_ARC)
{
ndot = ico_dot_arc(densit);
}
else
{
- WARNING("make_unsp: mode %c%d not allowed", (k) ? '+' : '-', mode);
- return 1;
+ GMX_RELEASE_ASSERT(false, "Invalid unit sphere mode");
}
last_n_dot = ndot; last_densit = densit; last_unsp = mode;
- *num_dot = ndot; if (k)
+ *num_dot = ndot;
+ if (k)
{
- return 0;
+ return;
}
/* in the following the dots of the unit sphere may be resorted */
} /* cycle i */
sfree(ico_wk);
sfree(work);
-
- return 0;
}
real dot;
} Neighb;
-int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
- int densit, int mode,
- real *value_of_area, real **at_area,
- real *value_of_vol,
- real **lidots, int *nu_dots,
- atom_id index[], int ePBC, matrix box)
+// This is extern "C" for now to make it easy to put valgrind suppressions.
+extern "C" void
+nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
+ int densit, int mode,
+ real *value_of_area, real **at_area,
+ real *value_of_vol,
+ real **lidots, int *nu_dots,
+ atom_id index[], int ePBC, matrix box)
{
int iat, i, ii, iii, ix, iy, iz, ixe, ixs, iye, iys, ize, izs, i_ac;
int jat, j, jj, jjj, jx, jy, jz;
if (distribution != -last_unsp || last_cubus != 4 ||
(densit != last_densit && densit != last_n_dot))
{
- if (make_unsp(densit, (-distribution), &n_dot, 4))
- {
- return 1;
- }
+ make_unsp(densit, (-distribution), &n_dot, 4);
}
xus = xpunsp;
/* calculate neighbour list with the box algorithm */
if (nat == 0)
{
- WARNING("nsc_dclm: no surface atoms selected");
- return 1;
+ return;
}
if (mode & FLAG_VOLUME)
{
{
fprintf(debug, "area=%8.3f\n", area);
}
-
- return 0;
}
+namespace gmx
+{
+
+class SurfaceAreaCalculator::Impl
+{
+ public:
+ Impl() : dotCount_(32), flags_(0)
+ {
+ }
+
+ int dotCount_;
+ int flags_;
+};
+
+SurfaceAreaCalculator::SurfaceAreaCalculator()
+ : impl_(new Impl())
+{
+}
-#if TEST_NSC > 0
-#define NAT 2
-main () {
+SurfaceAreaCalculator::~SurfaceAreaCalculator()
+{
+}
- int i, j, ndots;
- real co[3*NAT], ra[NAT], area, volume, a, b, c;
- real * dots;
- real * at_area;
- FILE *fp;
+void SurfaceAreaCalculator::setDotCount(int dotCount)
+{
+ impl_->dotCount_ = dotCount;
+}
+void SurfaceAreaCalculator::setCalculateVolume(bool bVolume)
+{
+ if (bVolume)
+ {
+ impl_->flags_ |= FLAG_VOLUME;
+ }
+ else
+ {
+ impl_->flags_ &= ~FLAG_VOLUME;
+ }
+}
- a = 1.; c = 0.1;
- fp = fopen("nsc.txt", "w+");
- for (i = 1; i <= NAT; i++)
+void SurfaceAreaCalculator::setCalculateAtomArea(bool bAtomArea)
+{
+ if (bAtomArea)
{
- j = i-1;
- co[3*i-3] = j*1*c;
- co[3*i-2] = j*1*c;
- co[3*i-1] = j*1*c;
- /*
- co[3*i-3] = i*1.4;
- co[3*i-2] = 0.;
- co[3*i-1] = 0.;
- */
- /*
- co[3*i-2] = a*0.3;
- a = -a; b=0;
- if (i%3 == 0) b=0.5;
- co[3*i-1] = b;
- ra[i-1] = 2.0;
- */
- ra[i-1] = (1.+j*0.5)*c;
+ impl_->flags_ |= FLAG_ATOM_AREA;
}
- /*
- if (NSC(co, ra, NAT, 42, NULL, &area,
- */
- if (NSC(co, ra, NAT, 42, NULL, &area,
- NULL, NULL, NULL, NULL))
+ else
{
- ERROR("error in NSC");
+ impl_->flags_ &= ~FLAG_ATOM_AREA;
}
- fprintf(fp, "\n");
- fprintf(fp, "area : %8.3f\n", area);
- fprintf(fp, "\n");
- fprintf(fp, "\n");
- fprintf(fp, "next call\n");
- fprintf(fp, "\n");
- fprintf(fp, "\n");
-
- if (NSC(co, ra, NAT, 42, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, &area,
- &at_area, &volume,
- &dots, &ndots))
+}
+
+void SurfaceAreaCalculator::setCalculateSurfaceDots(bool bDots)
+{
+ if (bDots)
+ {
+ impl_->flags_ |= FLAG_DOTS;
+ }
+ else
{
- ERROR("error in NSC");
+ impl_->flags_ &= ~FLAG_DOTS;
}
+}
- fprintf(fp, "\n");
- fprintf(fp, "area : %8.3f\n", area);
- printf("area : %8.3f\n", area);
- fprintf(fp, "volume : %8.3f\n", volume);
- printf("volume : %8.3f\n", volume);
- fprintf(fp, "ndots : %8d\n", ndots);
- printf("ndots : %8d\n", ndots);
- fprintf(fp, "\n");
- for (i = 1; i <= NAT; i++)
+void SurfaceAreaCalculator::calculate(
+ const rvec *x, const real *radius, const t_pbc *pbc,
+ int nat, atom_id index[], int flags, real *area, real *volume,
+ real **at_area, real **lidots, int *n_dots) const
+{
+ flags |= impl_->flags_;
+ *area = 0;
+ if (volume == NULL)
{
- fprintf(fp, "%4d ATOM %7.2f %7.2f %7.2f ra=%4.1f area=%8.3f\n",
- i, co[3*i-3], co[3*i-2], co[3*i-1], ra[i-1], at_area[i-1]);
+ flags &= ~FLAG_VOLUME;
}
- fprintf(fp, "\n");
- fprintf(fp, "DOTS : %8d\n", ndots);
- for (i = 1; i <= ndots; i++)
+ else
{
- fprintf(fp, "%4d DOTS %8.2f %8.2f %8.2f\n",
- i, dots[3*i-3], dots[3*i-2], dots[3*i-1]);
+ *volume = 0;
}
+ if (at_area == NULL)
+ {
+ flags &= ~FLAG_ATOM_AREA;
+ }
+ else
+ {
+ *at_area = NULL;
+ }
+ if (lidots == NULL)
+ {
+ flags &= ~FLAG_DOTS;
+ }
+ else
+ {
+ *lidots = NULL;
+ }
+ if (n_dots == NULL)
+ {
+ flags &= ~FLAG_DOTS;
+ }
+ else
+ {
+ *n_dots = 0;
+ }
+ nsc_dclm_pbc(x, const_cast<real *>(radius), nat, impl_->dotCount_,
+ flags, area, at_area, volume, lidots, n_dots, index,
+ pbc != NULL ? pbc->ePBC : epbcNONE,
+ pbc != NULL ? const_cast<rvec *>(pbc->box) : NULL);
}
-#endif
+
+} // namespace gmx
#define GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/classhelpers.h"
+
+struct t_pbc;
#define FLAG_DOTS 01
#define FLAG_VOLUME 02
#define FLAG_ATOM_AREA 04
-#ifdef __cplusplus
-extern "C"
+namespace gmx
{
-#endif
-
-int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
- int densit, int mode,
- real *value_of_area, real **at_area,
- real *value_of_vol,
- real **lidots, int *nu_dots,
- atom_id index[], int ePBC, matrix box);
-
-/*
- User notes :
- The input requirements :
- The arrays with atom coordinates and radii are thought to start
- with index 0, i.e., places 0, 1, and 2 are the x-, y-, and z-
- coordinates of the zero-th atom and place 0 in the other array
- is its radius.
-
- PLEASE TAKE INTO ACCOUNT THAT THE RADII GIVEN HERE ARE DIRECTLY
- USED FOR SURFACE CALCULATION. NSC does not increment with a probe
- radius.
-
- The user can define any number of dots. The program selects a
- dot density that is the lowest possible with at least the required
- number of dots. The points are distributed in accordance with the
- icosahedron-based or the dodecahedron-based method as described in
- ref. 1.
-
- The output requirements are :
- 1 and 3 : pointer to an existing real
- 2 and 4 : pointer to an existing pointer to real
- NSC allocates memory for an array
- 5 : pointer to an existing integer
-
- The subroutine NSC makes use of variant 2 described in reference 1.
- By selecting the necessary output via flags, the requirements for
- cpu-time and computer memory can be adapted to the actual needs.
-
- Example : flag = FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS
- The routine calculates the area, volume and the dot surface. The
- program allocates arrays for the atomwise areas and for the surface
- dots. The addresses are returned in the pointers to pointers to
- real.
- This variant is not recommended because normally the dot surface
- is needed for low point density (e.g.42) at which area and volume
- are inaccurate. The sign "|" is used as binary AND !
-
- flag = FLAG_VOLUME | FLAG_ATOM_AREA
- In this case the large arrays for storing the surface dots
- are not allocated. A large point number of the fully accessible
- sphere can be selected. Good accuracy is already achieved with
- 600-700 points per sphere (accuracy of about 1.5 square Angstrem
- per atomic sphere).
- Output pointers 4 and 5 may be NULL.
-
- flag = FLAG_DOTS
- Only the dot surface is produced.
- Output pointers 2 and 3 may be NULL.
-
- The output pointer 1 cannot be set to NULL in any circumstances. The
- overall area value is returned in every mode.
-
- All files calling NSC should include surfacearea.h !!
-
-
- Example for calling NSC (contents of user file):
-
- ...
- #include "surfacearea.h"
-
- int routine_calling_NSC(int n_atom, real *coordinates, real *radii) {
- real area, volume, *atomwise_area, *surface_dots;
- int i, density = 300, n_dots;
-
- ...
-
- for (i=0; i<n_atom; i++) {
- radii[i] += 1.4 /# add the probe radius if necessary #/
-
- if (NSC(coordinates, radii, n_atom, density,
- FLAG_AREA | FLAG_VOLUME | FLAG_DOTS,
- &area, &atomwise_area, &volume, &surface_dots, &n_dots))
- printf("error occured\n");
- return 1;
- }
-
- ...
-
- /# do something with areas, volume and surface dots #/
-
- ...
-
- return 0;
- }
+/*! \internal
+ * \brief
+ * Computes surface areas for a group of atoms/spheres.
+ *
+ * This class provides a surface area/volume calculator.
+ *
+ * The algorithm is based on representing each atom/sphere surface as a set of
+ * dots, and determining which dots are on the surface (not covered by any
+ * other atom/sphere). The dots are distributed evenly using an icosahedron- or
+ * a dodecahedron-based method (see the original reference cited in the code).
+ * The area is then estimated from the area represented by each dot.
+ * The volume is calculated by selecting a fixed point and integrating over the
+ * surface dots, summing up the cones whose tip is at the fixed point and base
+ * at the surface points.
+ *
+ * The default dot density per sphere is 32, which gives quite inaccurate
+ * areas and volumes, but a reasonable number of surface points. According to
+ * original documentation of the method, a density of 600-700 dots gives an
+ * accuracy of 1.5 A^2 per atom.
+ *
+ * \ingroup module_trajectoryanalysis
*/
-
-#ifdef __cplusplus
-}
-#endif
+class SurfaceAreaCalculator
+{
+ public:
+ /*! \brief
+ * Initializes a surface area calculator.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ SurfaceAreaCalculator();
+ ~SurfaceAreaCalculator();
+
+ /*! \brief
+ * Sets the number of surface dots per sphere to use.
+ *
+ * If not called, the default is 32.
+ */
+ void setDotCount(int dotCount);
+
+ /*! \brief
+ * Requests calculation of volume.
+ *
+ * If not called, and FLAG_VOLUME is not passed to calculate(), the
+ * volume output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateVolume(bool bVolume);
+ /*! \brief
+ * Requests output of per-atom areas.
+ *
+ * If not called, and FLAG_ATOM_AREA is not passed to calculate(), the
+ * atom area output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateAtomArea(bool bAtomArea);
+ /*! \brief
+ * Requests output of all surface dots.
+ *
+ * If not called, and FLAG_DOTS is not passed to calculate(), the
+ * surface dot output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateSurfaceDots(bool bDots);
+
+ /*! \brief
+ * Calculates the surface area for a set of positions.
+ *
+ * \param[in] x Atom positions (sphere centers).
+ * \param[in] radius Radius for each atom/sphere.
+ * These radii are used as-is, without adding any probe radius.
+ * \param[in] pbc PBC information (if `NULL`, calculation is done
+ * without PBC).
+ * \param[in] nat Number of atoms to calculate.
+ * \param[in] index Atom indices to include in the calculation.
+ * \param[in] flags Additional flags for the calculation.
+ * \param[out] area Total surface area (must be non-`NULL`).
+ * \param[out] volume Total volume (can be `NULL`).
+ * \param[out] at_area Surface area for each atom in \p index
+ * (\p nat values) (can be `NULL`).
+ * \param[out] lidots Surface dots as x,y,z triplets (`3*lidots` values)
+ * (can be `NULL`).
+ * \param[out] n_dots Number of surface dots in \p lidots
+ * (can be `NULL`).
+ *
+ * Calculates the surface area of spheres centered at `x[index[0]]`,
+ * ..., `x[index[nat-1]]`, with radii `radius[index[0]]`, ....
+ *
+ * If \p flags is 0, the calculation is done for the items specified
+ * with setCalculateVolume(), setCalculateAtomArea(), and
+ * setCalculateSurfaceDots(). Flags can specify FLAG_VOLUME,
+ * FLAG_ATOM_AREA, and/or FLAG_DOTS to request additional output for
+ * this particular calculation. If any output is `NULL`, that output
+ * is not calculated, irrespective of the calculation mode set.
+ *
+ * \todo
+ * Make the output options more C++-like, in particular for the array
+ * outputs.
+ *
+ * \todo
+ * Make this thread-safe; currently, only a single concurrent call to
+ * calculate() is supported.
+ */
+ void calculate(const rvec *x, const real *radius, const t_pbc *pbc,
+ int nat, atom_id index[], int flags, real *area,
+ real *volume, real **at_area,
+ real **lidots, int *n_dots) const;
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
#endif
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <SASA Name="Surface">
+ <Real Name="Area">12.566370614359172</Real>
+ <Sequence Name="Dots">
+ <Int Name="Length">36</Int>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>-1</Real>
+ <Real>-0.27639310998086691</Real>
+ <Real>-0.85065087452807109</Real>
+ <Real>-0.44721352665112024</Real>
+ <Real>0.72360690737127242</Real>
+ <Real>-0.52573101980466264</Real>
+ <Real>-0.44721352665112024</Real>
+ <Real>-0.8944272254243314</Real>
+ <Real>0</Real>
+ <Real>-0.44721352665112024</Real>
+ <Real>0.72360681651420888</Real>
+ <Real>0.52573114485870043</Real>
+ <Real>-0.44721352665112024</Real>
+ <Real>-0.27639325699069922</Real>
+ <Real>0.85065082676168668</Real>
+ <Real>-0.44721352665112024</Real>
+ <Real>0.27639333049561254</Real>
+ <Real>-0.85065080287848482</Real>
+ <Real>0.44721352665112024</Real>
+ <Real>-0.72360677108566906</Real>
+ <Real>-0.52573120738571333</Real>
+ <Real>0.44721352665112024</Real>
+ <Real>0.8944272254243314</Real>
+ <Real>0</Real>
+ <Real>0.44721352665112024</Real>
+ <Real>-0.72360686194274337</Real>
+ <Real>0.52573108233168353</Real>
+ <Real>0.44721352665112024</Real>
+ <Real>0.27639318348578412</Real>
+ <Real>0.85065085064488211</Real>
+ <Real>0.44721352665112024</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>1</Real>
+ </Sequence>
+ </SASA>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <SASA Name="Surface">
+ <Real Name="Area">12.566370614359172</Real>
+ <Sequence Name="Dots">
+ <Int Name="Length">366</Int>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>-1</Real>
+ <Real>0.099017100750074208</Real>
+ <Real>-0.30474315751655773</Real>
+ <Real>-0.94727357278976609</Real>
+ <Real>-0.25923000773171251</Real>
+ <Real>-0.18834164910928383</Real>
+ <Real>-0.94727357521584643</Real>
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#include "gromacs/trajectoryanalysis/modules/surfacearea.h"
+#include <cstdlib>
+
#include <gtest/gtest.h>
#include "gromacs/math/utilities.h"
dotCount_ = 0;
sfree(dots_);
dots_ = NULL;
- ASSERT_EQ(0, nsc_dclm_pbc(x_, &radius_[0], index_.size(), ndots, flags,
- &area_, &atomArea_, &volume_, &dots_, &dotCount_,
- &index_[0], epbcXYZ, bPBC ? box_ : NULL));
+ t_pbc pbc;
+ if (bPBC)
+ {
+ set_pbc(&pbc, epbcXYZ, box_);
+ }
+ ASSERT_NO_THROW_GMX(
+ {
+ gmx::SurfaceAreaCalculator calculator;
+ calculator.setDotCount(ndots);
+ calculator.calculate(x_, &radius_[0], bPBC ? &pbc : NULL,
+ index_.size(), &index_[0], flags,
+ &area_, &volume_, &atomArea_,
+ &dots_, &dotCount_);
+ });
}
real resultArea() const { return area_; }
real resultVolume() const { return volume_; }
{
if (checkDotCoordinates)
{
+ // The algorithm may produce the dots in different order in
+ // single and double precision due to some internal
+ // sorting...
+ std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
compound.checkSequenceArray(3*dotCount_, dots_, "Dots");
}
else
matrix box_;
private:
+ static int dotComparer(const void *a, const void *b)
+ {
+ for (int d = DIM - 1; d >= 0; --d)
+ {
+ const real ad = reinterpret_cast<const real *>(a)[d];
+ const real bd = reinterpret_cast<const real *>(b)[d];
+ // A fudge factor is needed to get an ordering that is the same
+ // in single and double precision, since the points are not
+ // exactly on the same Z plane even though in exact arithmetic
+ // they probably would be.
+ if (ad < bd - 0.001)
+ {
+ return -1;
+ }
+ else if (ad > bd + 0.001)
+ {
+ return 1;
+ }
+ }
+ return 0;
+ }
+
gmx_rng_t rng_;
int allocated_;
rvec *x_;
EXPECT_REAL_EQ_TOL(2*M_PI*(dist - 0.5 + 2)*2, atomArea(1), tolerance);
}
+TEST_F(SurfaceAreaTest, SurfacePoints12)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ reserveSpace(1);
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints32)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ reserveSpace(1);
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints42)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ reserveSpace(1);
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints122)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ reserveSpace(1);
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
TEST_F(SurfaceAreaTest, Computes100Points)
{
gmx::test::TestReferenceChecker checker(data_.rootChecker());
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff