/*******************************************************************************
* Find separation vector between two pos vectors
*******************************************************************************/
static PyObject*
separationVector(PyObject *self, PyObject *args)
{
int length, *PBC;
double *returnVector, *pos1, *pos2, *cellDims;
PyArrayObject *PBCIn=NULL;
PyArrayObject *returnVectorIn=NULL;
PyArrayObject *pos1In=NULL;
PyArrayObject *pos2In=NULL;
PyArrayObject *cellDimsIn=NULL;
int i;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!O!O!O!", &PyArray_Type, &returnVectorIn, &PyArray_Type, &pos1In,
&PyArray_Type, &pos2In, &PyArray_Type, &cellDimsIn, &PyArray_Type, &PBCIn))
return NULL;
if (not_intVector(PBCIn)) return NULL;
PBC = pyvector_to_Cptr_int(PBCIn);
if (not_doubleVector(pos1In)) return NULL;
pos1 = pyvector_to_Cptr_double(pos1In);
length = ((int) PyArray_DIM(pos1In, 0)) / 3;
if (not_doubleVector(pos2In)) return NULL;
pos2 = pyvector_to_Cptr_double(pos2In);
if (not_doubleVector(returnVectorIn)) return NULL;
returnVector = pyvector_to_Cptr_double(returnVectorIn);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
/* loop */
for (i = 0; i < length; i++)
{
double atomSepVec[3];
atomSeparationVector(atomSepVec, pos1[3*i], pos1[3*i+1], pos1[3*i+2], pos2[3*i], pos2[3*i+1], pos2[3*i+2],
cellDims[0], cellDims[4], cellDims[8], PBC[0], PBC[1], PBC[2]);
returnVector[3*i] = atomSepVec[0];
returnVector[3*i+1] = atomSepVec[1];
returnVector[3*i+2] = atomSepVec[2];
}
return Py_BuildValue("i", 0);
}
/*******************************************************************************
** Make scalars array for visible atoms
*******************************************************************************/
static PyObject*
makeVisibleScalarArray(PyObject *self, PyObject *args)
{
int NVisible;
PyArrayObject *visibleAtoms=NULL;
PyArrayObject *scalarsFull=NULL;
int i;
npy_intp numpydims[1];
PyArrayObject *scalars=NULL;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!", &PyArray_Type, &visibleAtoms, &PyArray_Type, &scalarsFull))
return NULL;
if (not_intVector(visibleAtoms)) return NULL;
NVisible = (int) PyArray_DIM(visibleAtoms, 0);
if (not_doubleVector(scalarsFull)) return NULL;
/* create radius array */
numpydims[0] = (npy_intp) NVisible;
scalars = (PyArrayObject *) PyArray_SimpleNew(1, numpydims, NPY_FLOAT64);
/* populate array */
for (i = 0; i < NVisible; i++)
{
int index;
index = IIND1(visibleAtoms, i);
DIND1(scalars, i) = DIND1(scalarsFull, index);
}
return PyArray_Return(scalars);
}
/*******************************************************************************
* Return the magnitude of given vector
*******************************************************************************/
static PyObject*
magnitude(PyObject *self, PyObject *args)
{
int length;
double *pos;
PyArrayObject *posIn=NULL;
int i;
double sum;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!", &PyArray_Type, &posIn))
return NULL;
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
length = (int) PyArray_DIM(posIn, 0);
/* compute */
sum = 0.0;
for (i = 0; i < length; i++)
sum += pos[i] * pos[i];
return Py_BuildValue("d", sqrt(sum));
}
/*******************************************************************************
* return magnitude of separation vector between two pos vectors
*******************************************************************************/
static PyObject*
separationMagnitude(PyObject *self, PyObject *args)
{
int length, *PBC;
double *pos1, *pos2, *cellDims;
PyArrayObject *PBCIn=NULL;
PyArrayObject *pos1In=NULL;
PyArrayObject *pos2In=NULL;
PyArrayObject *cellDimsIn=NULL;
int i;
double sum;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!O!O!", &PyArray_Type, &pos1In, &PyArray_Type, &pos2In,
&PyArray_Type, &cellDimsIn, &PyArray_Type, &PBCIn))
return NULL;
if (not_intVector(PBCIn)) return NULL;
PBC = pyvector_to_Cptr_int(PBCIn);
if (not_doubleVector(pos1In)) return NULL;
pos1 = pyvector_to_Cptr_double(pos1In);
length = ((int) PyArray_DIM(pos1In, 0)) / 3;
if (not_doubleVector(pos2In)) return NULL;
pos2 = pyvector_to_Cptr_double(pos2In);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
/* loop */
sum = 0;
for (i = 0; i < length; i++ )
{
double r2;
r2 = atomicSeparation2( pos1[3*i], pos1[3*i+1], pos1[3*i+2], pos2[3*i], pos2[3*i+1], pos2[3*i+2], cellDims[0], cellDims[4], cellDims[8], PBC[0], PBC[1], PBC[2]);
sum += r2;
}
return Py_BuildValue("d", sqrt(sum));
}
/*******************************************************************************
** Make points array for visible atoms
*******************************************************************************/
static PyObject*
makeVisiblePointsArray(PyObject *self, PyObject *args)
{
int NVisible;
PyArrayObject *visibleAtoms=NULL;
PyArrayObject *pos=NULL;
int i;
npy_intp numpydims[2];
PyArrayObject *visiblePos=NULL;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!", &PyArray_Type, &visibleAtoms, &PyArray_Type, &pos))
return NULL;
if (not_intVector(visibleAtoms)) return NULL;
NVisible = (int) PyArray_DIM(visibleAtoms, 0);
if (not_doubleVector(pos)) return NULL;
/* create radius array */
numpydims[0] = (npy_intp) NVisible;
numpydims[1] = 3;
visiblePos = (PyArrayObject *) PyArray_SimpleNew(2, numpydims, NPY_FLOAT64);
/* populate array */
for (i = 0; i < NVisible; i++)
{
int index, index3, j;
index = IIND1(visibleAtoms, i);
index3 = index * 3;
for (j = 0; j < 3; j++)
DIND2(visiblePos, i, j) = DIND1(pos, index3 + j);
}
return PyArray_Return(visiblePos);
}
/*******************************************************************************
** Make arrays for rendering bonds for displacment vectors
*******************************************************************************/
static PyObject*
makeDisplacementVectorBondsArrays(PyObject *self, PyObject *args)
{
int numBonds;
PyArrayObject *visibleAtoms=NULL;
PyArrayObject *scalarsArray=NULL;
PyArrayObject *pos=NULL;
PyArrayObject *drawBondArray=NULL;
PyArrayObject *bondVectorsArray=NULL;
PyObject *result=NULL;
/* parse arguments from Python */
if (PyArg_ParseTuple(args, "iO!O!O!O!O!", &numBonds, &PyArray_Type, &visibleAtoms, &PyArray_Type, &scalarsArray,
&PyArray_Type, &pos, &PyArray_Type, &drawBondArray, &PyArray_Type, &bondVectorsArray))
{
int i, count, numVisible;
npy_intp numpydims[2];
PyArrayObject *bondCoords = NULL;
PyArrayObject *bondScalars = NULL;
PyArrayObject *bondVectors = NULL;
/* check arguments */
if (not_intVector(visibleAtoms)) return NULL;
numVisible = (int) PyArray_DIM(visibleAtoms, 0);
if (not_doubleVector(scalarsArray)) return NULL;
if (not_doubleVector(pos)) return NULL;
if (not_intVector(drawBondArray)) return NULL;
if (not_doubleVector(bondVectorsArray)) return NULL;
/* create array for bond coordinates */
numpydims[0] = (npy_intp) numBonds;
numpydims[1] = 3;
bondCoords = (PyArrayObject *) PyArray_SimpleNew(2, numpydims, NPY_FLOAT64);
if (bondCoords == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondCoords");
return NULL;
}
/* create array for bond vectors */
numpydims[0] = (npy_intp) numBonds;
numpydims[1] = 3;
bondVectors = (PyArrayObject *) PyArray_SimpleNew(2, numpydims, NPY_FLOAT64);
if (bondVectors == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondVectors");
Py_DECREF(bondCoords);
return NULL;
}
/* create array for bond scalars */
numpydims[0] = (npy_intp) numBonds;
bondScalars = (PyArrayObject *) PyArray_SimpleNew(1, numpydims, NPY_FLOAT64);
if (bondScalars == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondScalars");
Py_DECREF(bondCoords);
Py_DECREF(bondVectors);
return NULL;
}
/* loop over visible atoms */
count = 0;
for (i = 0; i < numVisible; i++)
{
/* check if we should be drawing this bond */
if (IIND1(drawBondArray, i))
{
int j, i3 = 3 * i;
int index3 = 3 * IIND1(visibleAtoms, i);
/* store bond values */
for (j = 0; j < 3; j++)
{
DIND2(bondCoords, count, j) = DIND1(pos, index3 + j);
DIND2(bondVectors, count, j) = DIND1(bondVectorsArray, i3 + j);
}
DIND1(bondScalars, count) = DIND1(scalarsArray, i);
count++;
}
}
/* tuple for result */
result = PyTuple_New(3);
PyTuple_SetItem(result, 0, PyArray_Return(bondCoords));
PyTuple_SetItem(result, 1, PyArray_Return(bondVectors));
PyTuple_SetItem(result, 2, PyArray_Return(bondScalars));
}
return result;
}
/*******************************************************************************
** Split visible atoms by specie (position and scalar)
*******************************************************************************/
static PyObject*
splitVisAtomsBySpecie(PyObject *self, PyObject *args)
{
int NVisible, *visibleAtoms, NSpecies, *specieArray, *specieCount, scalarType, heightAxis, vectorsLen;
double *pos, *PE, *KE, *charge, *scalars;
PyArrayObject *visibleAtomsIn=NULL;
PyArrayObject *specieArrayIn=NULL;
PyArrayObject *specieCountIn=NULL;
PyArrayObject *posIn=NULL;
PyArrayObject *PEIn=NULL;
PyArrayObject *KEIn=NULL;
PyArrayObject *chargeIn=NULL;
PyArrayObject *scalarsIn=NULL;
PyArrayObject *vectors=NULL;
int i, j, index, specie, count;
npy_intp numpyDims[2];
double scalar;
PyObject *list=NULL;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!iO!O!O!O!O!O!O!iiO!", &PyArray_Type, &visibleAtomsIn, &NSpecies, &PyArray_Type, &specieArrayIn,
&PyArray_Type, &specieCountIn, &PyArray_Type, &posIn, &PyArray_Type, &PEIn, &PyArray_Type, &KEIn, &PyArray_Type,
&chargeIn, &PyArray_Type, &scalarsIn, &scalarType, &heightAxis, &PyArray_Type, &vectors))
return NULL;
if (not_intVector(visibleAtomsIn)) return NULL;
visibleAtoms = pyvector_to_Cptr_int(visibleAtomsIn);
NVisible = (int) PyArray_DIM(visibleAtomsIn, 0);
if (not_intVector(specieArrayIn)) return NULL;
specieArray = pyvector_to_Cptr_int(specieArrayIn);
if (not_intVector(specieCountIn)) return NULL;
specieCount = pyvector_to_Cptr_int(specieCountIn);
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
if (not_doubleVector(PEIn)) return NULL;
PE = pyvector_to_Cptr_double(PEIn);
if (not_doubleVector(KEIn)) return NULL;
KE = pyvector_to_Cptr_double(KEIn);
if (not_doubleVector(chargeIn)) return NULL;
charge = pyvector_to_Cptr_double(chargeIn);
if (not_doubleVector(scalarsIn)) return NULL;
scalars = pyvector_to_Cptr_double(scalarsIn);
if (not_doubleVector(vectors)) return NULL;
vectorsLen = (int) PyArray_DIM(vectors, 0);
/* first pass to get counters, assume counter zeroed before */
for (i = 0; i < NVisible; i++)
{
index = visibleAtoms[i];
specie = specieArray[index];
specieCount[specie]++;
}
/* create list for returning */
list = PyList_New(NSpecies);
/* loop over species */
for (i = 0; i < NSpecies; i++)
{
PyArrayObject *speciePos = NULL;
PyArrayObject *specieScalars = NULL;
PyArrayObject *specieVectors = NULL;
PyObject *tuple = NULL;
/* allocate position array */
numpyDims[0] = (npy_intp) specieCount[i];
numpyDims[1] = 3;
speciePos = (PyArrayObject *) PyArray_SimpleNew(2, numpyDims, NPY_FLOAT64);
/* allocate position array */
numpyDims[0] = (npy_intp) specieCount[i];
specieScalars = (PyArrayObject *) PyArray_SimpleNew(1, numpyDims, NPY_FLOAT64);
if (vectorsLen > 0)
{
/* allocate vectors array */
numpyDims[0] = (npy_intp) specieCount[i];
numpyDims[1] = 3;
specieVectors = (PyArrayObject *) PyArray_SimpleNew(2, numpyDims, NPY_FLOAT64);
}
else
{
numpyDims[0] = 0;
specieVectors = (PyArrayObject *) PyArray_SimpleNew(1, numpyDims, NPY_FLOAT64);
}
/* loop over atoms */
count = 0;
for (j = 0; j < NVisible; j++)
{
index = visibleAtoms[j];
specie = specieArray[index];
if (specie == i)
{
/* position */
DIND2(speciePos, count, 0) = pos[3*index+0];
DIND2(speciePos, count, 1) = pos[3*index+1];
DIND2(speciePos, count, 2) = pos[3*index+2];
/* scalar */
if (scalarType == 0) scalar = specie;
else if (scalarType == 1) scalar = pos[3*index+heightAxis];
else if (scalarType == 2) scalar = KE[index];
else if (scalarType == 3) scalar = PE[index];
else if (scalarType == 4) scalar = charge[index];
else scalar = scalars[j];
DIND1(specieScalars, count) = scalar;
if (vectorsLen > 0)
{
/* vector */
DIND2(specieVectors, count, 0) = DIND2(vectors, index, 0);
DIND2(specieVectors, count, 1) = DIND2(vectors, index, 1);
DIND2(specieVectors, count, 2) = DIND2(vectors, index, 2);
}
count++;
}
}
/* create tuple (setItem steals ownership of array objects!!??) */
tuple = PyTuple_New(3);
PyTuple_SetItem(tuple, 0, PyArray_Return(speciePos));
PyTuple_SetItem(tuple, 1, PyArray_Return(specieScalars));
PyTuple_SetItem(tuple, 2, PyArray_Return(specieVectors));
/* store in list (setItem steals ownership of tuple!?) */
PyList_SetItem(list, i, tuple);
}
return list;
}
/*******************************************************************************
** Make arrays for rendering bonds
*******************************************************************************/
static PyObject*
makeBondsArrays(PyObject *self, PyObject *args)
{
PyArrayObject *visibleAtoms=NULL;
PyArrayObject *scalarsArray=NULL;
PyArrayObject *pos=NULL;
PyArrayObject *numBondsArray=NULL;
PyArrayObject *bondsArray=NULL;
PyArrayObject *bondVectorsArray=NULL;
PyObject *result=NULL;
/* parse arguments from Python */
if (PyArg_ParseTuple(args, "O!O!O!O!O!O!", &PyArray_Type, &visibleAtoms, &PyArray_Type, &scalarsArray,
&PyArray_Type, &pos, &PyArray_Type, &numBondsArray, &PyArray_Type, &bondsArray, &PyArray_Type,
&bondVectorsArray))
{
int i, numVisible, numBonds, count, bondCount;
npy_intp numpydims[2];
PyArrayObject *bondCoords = NULL;
PyArrayObject *bondScalars = NULL;
PyArrayObject *bondVectors = NULL;
/* check arguments */
if (not_intVector(visibleAtoms)) return NULL;
numVisible = (int) PyArray_DIM(visibleAtoms, 0);
if (not_doubleVector(scalarsArray)) return NULL;
if (not_doubleVector(pos)) return NULL;
if (not_intVector(numBondsArray)) return NULL;
if (not_intVector(bondsArray)) return NULL;
if (not_doubleVector(bondVectorsArray)) return NULL;
/* calculate the number of bonds */
numBonds = 0;
for (i = 0; i < numVisible; i++) numBonds += IIND1(numBondsArray, i);
/* multiply by two as there are two "bonds" drawn per real bond */
numBonds *= 2;
/* create array for bond coordinates */
numpydims[0] = (npy_intp) numBonds;
numpydims[1] = 3;
bondCoords = (PyArrayObject *) PyArray_SimpleNew(2, numpydims, NPY_FLOAT64);
if (bondCoords == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondCoords");
return NULL;
}
/* create array for bond vectors */
numpydims[0] = (npy_intp) numBonds;
numpydims[1] = 3;
bondVectors = (PyArrayObject *) PyArray_SimpleNew(2, numpydims, NPY_FLOAT64);
if (bondVectors == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondVectors");
Py_DECREF(bondCoords);
return NULL;
}
/* create array for bond scalars */
numpydims[0] = (npy_intp) numBonds;
bondScalars = (PyArrayObject *) PyArray_SimpleNew(1, numpydims, NPY_FLOAT64);
if (bondScalars == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate bondScalars");
Py_DECREF(bondCoords);
Py_DECREF(bondVectors);
return NULL;
}
/* loop over visible atoms */
count = 0;
bondCount = 0;
for (i = 0; i < numVisible; i++)
{
int j;
int indexa = IIND1(visibleAtoms, i);
int indexa3 = 3 * indexa;
int numBondsForAtom = IIND1(numBondsArray, i);
double xposa, yposa, zposa, scalara;
/* atom position and scalar */
xposa = DIND1(pos, indexa3 );
yposa = DIND1(pos, indexa3 + 1);
zposa = DIND1(pos, indexa3 + 2);
scalara = DIND1(scalarsArray, i);
/* loop over this atoms bonds */
for (j = 0; j < numBondsForAtom; j++)
{
int cnt3 = count * 3;
int visIndex = IIND1(bondsArray, count);
int indexb3 = 3 * IIND1(visibleAtoms, visIndex);
double xposb = DIND1(pos, indexb3 );
double yposb = DIND1(pos, indexb3 + 1);
double zposb = DIND1(pos, indexb3 + 2);
double scalarb = DIND1(scalarsArray, visIndex);
double bvecx = DIND1(bondVectorsArray, cnt3 );
double bvecy = DIND1(bondVectorsArray, cnt3 + 1);
double bvecz = DIND1(bondVectorsArray, cnt3 + 2);
/* partial bond from atom a towards b */
DIND2(bondCoords, bondCount, 0) = xposa;
DIND2(bondCoords, bondCount, 1) = yposa;
DIND2(bondCoords, bondCount, 2) = zposa;
DIND2(bondVectors, bondCount, 0) = bvecx;
DIND2(bondVectors, bondCount, 1) = bvecy;
DIND2(bondVectors, bondCount, 2) = bvecz;
DIND1(bondScalars, bondCount) = scalara;
bondCount++;
/* partial bond from atom b towards a */
DIND2(bondCoords, bondCount, 0) = xposb;
DIND2(bondCoords, bondCount, 1) = yposb;
DIND2(bondCoords, bondCount, 2) = zposb;
DIND2(bondVectors, bondCount, 0) = -1.0 * bvecx;
DIND2(bondVectors, bondCount, 1) = -1.0 * bvecy;
DIND2(bondVectors, bondCount, 2) = -1.0 * bvecz;
DIND1(bondScalars, bondCount) = scalarb;
bondCount++;
count++;
}
}
/* tuple for result */
result = PyTuple_New(3);
PyTuple_SetItem(result, 0, PyArray_Return(bondCoords));
PyTuple_SetItem(result, 1, PyArray_Return(bondVectors));
PyTuple_SetItem(result, 2, PyArray_Return(bondScalars));
}
return result;
}
/*******************************************************************************
** Check if an object has been picked
*******************************************************************************/
static PyObject*
pickObject(PyObject *self, PyObject *args)
{
int visibleAtomsDim, *visibleAtoms, vacsDim, *vacs, intsDim, *ints, onAntsDim, *onAnts, splitsDim, *splits;
int *PBC, *specie, *refSpecie;
double *pickPos, *pos, *refPos, *cellDims, *specieCovRad, *refSpecieCovRad, *result;
PyArrayObject *visibleAtomsIn=NULL;
PyArrayObject *vacsIn=NULL;
PyArrayObject *intsIn=NULL;
PyArrayObject *onAntsIn=NULL;
PyArrayObject *splitsIn=NULL;
PyArrayObject *pickPosIn=NULL;
PyArrayObject *posIn=NULL;
PyArrayObject *refPosIn=NULL;
PyArrayObject *PBCIn=NULL;
PyArrayObject *cellDimsIn=NULL;
PyArrayObject *specieIn=NULL;
PyArrayObject *refSpecieIn=NULL;
PyArrayObject *specieCovRadIn=NULL;
PyArrayObject *refSpecieCovRadIn=NULL;
PyArrayObject *resultIn=NULL;
int minSepIndex, minSepType;
double approxBoxWidth, minSepRad, minSep2, minSep;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!O!O!O!O!O!O!O!O!O!O!O!O!O!", &PyArray_Type, &visibleAtomsIn, &PyArray_Type, &vacsIn,
&PyArray_Type, &intsIn, &PyArray_Type, &onAntsIn, &PyArray_Type, &splitsIn, &PyArray_Type, &pickPosIn, &PyArray_Type,
&posIn, &PyArray_Type, &refPosIn, &PyArray_Type, &PBCIn, &PyArray_Type, &cellDimsIn, &PyArray_Type, &specieIn,
&PyArray_Type, &refSpecieIn, &PyArray_Type, &specieCovRadIn, &PyArray_Type, &refSpecieCovRadIn, &PyArray_Type,
&resultIn))
return NULL;
if (not_intVector(visibleAtomsIn)) return NULL;
visibleAtoms = pyvector_to_Cptr_int(visibleAtomsIn);
visibleAtomsDim = (int) PyArray_DIM(visibleAtomsIn, 0);
if (not_intVector(vacsIn)) return NULL;
vacs = pyvector_to_Cptr_int(vacsIn);
vacsDim = (int) PyArray_DIM(vacsIn, 0);
if (not_intVector(intsIn)) return NULL;
ints = pyvector_to_Cptr_int(intsIn);
intsDim = (int) PyArray_DIM(intsIn, 0);
if (not_intVector(onAntsIn)) return NULL;
onAnts = pyvector_to_Cptr_int(onAntsIn);
onAntsDim = (int) PyArray_DIM(onAntsIn, 0);
if (not_intVector(splitsIn)) return NULL;
splits = pyvector_to_Cptr_int(splitsIn);
splitsDim = (int) PyArray_DIM(splitsIn, 0);
if (not_doubleVector(pickPosIn)) return NULL;
pickPos = pyvector_to_Cptr_double(pickPosIn);
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
if (not_doubleVector(refPosIn)) return NULL;
refPos = pyvector_to_Cptr_double(refPosIn);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
if (not_intVector(PBCIn)) return NULL;
PBC = pyvector_to_Cptr_int(PBCIn);
if (not_intVector(specieIn)) return NULL;
specie = pyvector_to_Cptr_int(specieIn);
if (not_intVector(refSpecieIn)) return NULL;
refSpecie = pyvector_to_Cptr_int(refSpecieIn);
if (not_doubleVector(specieCovRadIn)) return NULL;
specieCovRad = pyvector_to_Cptr_double(specieCovRadIn);
if (not_doubleVector(refSpecieCovRadIn)) return NULL;
refSpecieCovRad = pyvector_to_Cptr_double(refSpecieCovRadIn);
if (not_doubleVector(resultIn)) return NULL;
result = pyvector_to_Cptr_double(resultIn);
// this should be detected automatically depending on cell size...
approxBoxWidth = 4.0;
/* initialise */
minSep2 = 9999999.0;
minSepIndex = -1;
minSepRad = 0.0;
minSepType = 0;
/* pick atoms (if there are any) */
if (visibleAtomsDim > 0)
{
int i, boxIndex, boxNebList[27], boxstat;
int boxNebListSize;
double *visPos;
struct Boxes *boxes;
#ifdef DEBUG
printf("PICKC: Picking atoms\n");
#endif
/* vis atoms pos */
visPos = malloc(3 * visibleAtomsDim * sizeof(double));
if (visPos == NULL)
{
PyErr_SetString(PyExc_RuntimeError, "Could not allocate visPos");
return NULL;
}
for (i = 0; i < visibleAtomsDim; i++)
{
int i3 = 3 * i;
int index = visibleAtoms[i];
int index3 = 3 * index;
visPos[i3 ] = pos[index3 ];
visPos[i3 + 1] = pos[index3 + 1];
visPos[i3 + 2] = pos[index3 + 2];
}
/* box vis atoms */
boxes = setupBoxes(approxBoxWidth, PBC, cellDims);
if (boxes == NULL)
{
free(visPos);
return NULL;
}
boxstat = putAtomsInBoxes(visibleAtomsDim, visPos, boxes);
if (boxstat)
{
free(visPos);
return NULL;
}
/* box index of picked pos */
boxIndex = boxIndexOfAtom(pickPos[0], pickPos[1], pickPos[2], boxes);
if (boxIndex < 0)
{
free(visPos);
freeBoxes(boxes);
return NULL;
}
/* neighbouring boxes */
boxNebListSize = getBoxNeighbourhood(boxIndex, boxNebList, boxes);
/* loop over neighbouring boxes, looking for nearest atom */
for (i = 0; i < boxNebListSize; i++)
{
int k;
int checkBox = boxNebList[i];
for (k = 0; k < boxes->boxNAtoms[checkBox]; k++)
{
int index, realIndex;
double sep2, rad;
index = boxes->boxAtoms[checkBox][k];
/* atomic separation */
sep2 = atomicSeparation2(pickPos[0], pickPos[1], pickPos[2],
visPos[3*index], visPos[3*index+1], visPos[3*index+2],
cellDims[0], cellDims[1], cellDims[2],
PBC[0], PBC[1], PBC[2]);
/* need radius too */
realIndex = visibleAtoms[index];
rad = specieCovRad[specie[realIndex]];
if (sep2 < minSep2)
{
minSep2 = sep2;
minSepIndex = index;
minSepRad = rad;
}
}
}
/* free memory */
free(visPos);
freeBoxes(boxes);
}
/* now check defects (if there are any) */
if (vacsDim + intsDim + onAntsDim + splitsDim > 0)
{
int i, NVis, count, boxNebListSize, minSepIsDefect;
int boxIndex, boxNebList[27], boxstat;
double *visPos, *visCovRad;
struct Boxes *boxes;
#ifdef DEBUG
printf("PICKC: Picking defect\n");
#endif
/* build positions array of all defects */
NVis = vacsDim + intsDim + onAntsDim + splitsDim;
visPos = malloc(3 * NVis * sizeof(double));
if (visPos == NULL)
{
PyErr_SetString(PyExc_RuntimeError, "Could not allocate visPos");
return NULL;
}
visCovRad = malloc(NVis * sizeof(double));
if (visCovRad == NULL)
{
PyErr_SetString(PyExc_RuntimeError, "Could not allocate visCovRad");
free(visPos);
return NULL;
}
/* add defects positions: vac then int then ant */
count = 0;
for (i = 0; i < vacsDim; i++)
{
int c3 = 3 * count;
int index = vacs[i];
int index3 = 3 * index;
visPos[c3 ] = refPos[index3 ];
visPos[c3 + 1] = refPos[index3 + 1];
visPos[c3 + 2] = refPos[index3 + 2];
visCovRad[count++] = refSpecieCovRad[refSpecie[index]] * 1.2; // * 0.75; // multiply by 0.75 because vacs aren't full size (rendering.py)
}
for (i = 0; i < intsDim; i++)
{
int c3 = 3 * count;
int index = ints[i];
int index3 = 3 * index;
visPos[c3 ] = pos[index3 ];
visPos[c3 + 1] = pos[index3 + 1];
visPos[c3 + 2] = pos[index3 + 2];
visCovRad[count++] = specieCovRad[specie[index]];
}
for (i = 0; i < onAntsDim; i++)
{
int c3 = 3 * count;
int index = onAnts[i];
int index3 = 3 * index;
visPos[c3 ] = pos[index3 ];
visPos[c3 + 1] = pos[index3 + 1];
visPos[c3 + 2] = pos[index3 + 2];
visCovRad[count++] = specieCovRad[specie[index]];
}
for (i = 0; i < splitsDim / 3; i++)
{
int i3 = 3 * i;
int index, c3, index3;
index = splits[i3 ];
index3 = index * 3;
c3 = count * 3;
visPos[c3 ] = refPos[index3 ];
visPos[c3 + 1] = refPos[index3 + 1];
visPos[c3 + 2] = refPos[index3 + 2];
visCovRad[count++] = refSpecieCovRad[refSpecie[index]];
index = splits[i3 + 1];
index3 = index * 3;
c3 = count * 3;
visPos[c3 ] = pos[index3 ];
visPos[c3 + 1] = pos[index3 + 1];
visPos[c3 + 2] = pos[index3 + 2];
visCovRad[count++] = specieCovRad[specie[index]];
index = splits[i3 + 2];
index3 = index * 3;
c3 = count * 3;
visPos[c3 ] = pos[index3 ];
visPos[c3 + 1] = pos[index3 + 1];
visPos[c3 + 2] = pos[index3 + 2];
visCovRad[count++] = specieCovRad[specie[index]];
}
/* box vis atoms */
boxes = setupBoxes(approxBoxWidth, PBC, cellDims);
if (boxes == NULL)
{
free(visPos);
free(visCovRad);
return NULL;
}
boxstat = putAtomsInBoxes(NVis, visPos, boxes);
if (boxstat)
{
free(visPos);
free(visCovRad);
return NULL;
}
/* box index of picked pos */
boxIndex = boxIndexOfAtom(pickPos[0], pickPos[1], pickPos[2], boxes);
if (boxIndex < 0)
{
free(visPos);
free(visCovRad);
freeBoxes(boxes);
return NULL;
}
/* neighbouring boxes */
boxNebListSize = getBoxNeighbourhood(boxIndex, boxNebList, boxes);
/* loop over neighbouring boxes, looking for nearest atom */
minSepIsDefect = 0;
for (i = 0; i < boxNebListSize; i++)
{
int k;
int checkBox = boxNebList[i];
for (k = 0; k < boxes->boxNAtoms[checkBox]; k++)
{
int index;
double sep2, rad;
index = boxes->boxAtoms[checkBox][k];
/* atomic separation */
sep2 = atomicSeparation2(pickPos[0], pickPos[1], pickPos[2],
visPos[3*index], visPos[3*index+1], visPos[3*index+2],
cellDims[0], cellDims[1], cellDims[2],
PBC[0], PBC[1], PBC[2]);
/* need radius too */
rad = visCovRad[index];
if (sep2 < minSep2)
{
minSep2 = sep2;
minSepIndex = index;
minSepRad = rad;
minSepIsDefect = 1;
}
}
}
if (minSepIsDefect)
{
/* picked type */
if (minSepIndex < vacsDim)
{
minSepType = 1;
}
else if (minSepIndex < vacsDim + intsDim)
{
minSepIndex -= vacsDim;
minSepType = 2;
}
else if (minSepIndex < vacsDim + intsDim + onAntsDim)
{
minSepIndex -= vacsDim + intsDim;
minSepType = 3;
}
else
{
minSepIndex -= vacsDim + intsDim + onAntsDim;
minSepIndex = (int) (minSepIndex / 3);
minSepType = 4;
}
}
/* free memory */
freeBoxes(boxes);
free(visPos);
free(visCovRad);
}
/* min separation */
minSep = sqrt(minSep2);
/* if separation is greater than radius, subtract radius,
* otherwise set to zero (within radius is good enough for me)
*/
minSep = (minSep > minSepRad) ? minSep - minSepRad : 0.0;
/* store result */
result[0] = minSepType;
result[1] = minSepIndex;
result[2] = minSep;
#ifdef DEBUG
printf("PICKC: End\n");
#endif
return Py_BuildValue("i", 0);
}
/*******************************************************************************
** Calculate the radial distribution function for the given selections of
** visible atoms.
**
** Inputs are:
** - visibleAtoms: indices of atoms that are to be used for the calculation
** - specie: array containing the species index for each atom
** - pos: array containing the positions of the atoms
** - specieID1: the species of the first selection of atoms
** - specieID2: the species of the second selection of atoms
** - cellDims: the size of the simulation cell
** - pbc: periodic boundary conditions
** - start: minimum separation to use when constructing the histogram
** - finish: maximum separation to use when constructing the histogram
** - interval: the interval between histogram bins
** - numBins: the number of histogram bins
** - rdf: the result is returned in this array
*******************************************************************************/
static PyObject*
calculateRDF(PyObject *self, PyObject *args)
{
int numVisible, *visibleAtoms, *specie, specieID1, specieID2, *pbc, numBins;
int numAtoms;
double *pos, *cellDims, start, finish, *rdf;
PyArrayObject *visibleAtomsIn=NULL;
PyArrayObject *specieIn=NULL;
PyArrayObject *pbcIn=NULL;
PyArrayObject *posIn=NULL;
PyArrayObject *cellDimsIn=NULL;
PyArrayObject *rdfIn=NULL;
int i, status, *sel1, *sel2, sel1cnt, sel2cnt, duplicates;
double interval;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!O!iiO!O!dddiO!", &PyArray_Type, &visibleAtomsIn, &PyArray_Type, &specieIn,
&PyArray_Type, &posIn, &specieID1, &specieID2, &PyArray_Type, &cellDimsIn, &PyArray_Type, &pbcIn, &start,
&finish, &interval, &numBins, &PyArray_Type, &rdfIn))
return NULL;
if (not_intVector(visibleAtomsIn)) return NULL;
visibleAtoms = pyvector_to_Cptr_int(visibleAtomsIn);
numVisible = (int) PyArray_DIM(visibleAtomsIn, 0);
if (not_intVector(specieIn)) return NULL;
specie = pyvector_to_Cptr_int(specieIn);
numAtoms = (int) PyArray_DIM(specieIn, 0);
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
if (not_doubleVector(rdfIn)) return NULL;
rdf = pyvector_to_Cptr_double(rdfIn);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
if (not_intVector(pbcIn)) return NULL;
pbc = pyvector_to_Cptr_int(pbcIn);
/* initialise result array to zero */
for (i = 0; i < numBins; i++) rdf[i] = 0.0;
/* create the selections of atoms and check for number of duplicates */
sel1 = malloc(numVisible * sizeof(int));
if (sel1 == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate sel1");
return NULL;
}
sel2 = malloc(numVisible * sizeof(int));
if (sel2 == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate sel2");
free(sel1);
return NULL;
}
sel1cnt = 0;
sel2cnt = 0;
duplicates = 0;
for (i = 0; i < numVisible; i++)
{
int index = visibleAtoms[i];
/* check if this atom is in the first selection (negative means all species) */
if (specieID1 < 0 || specie[index] == specieID1)
{
sel1[i] = 1;
sel1cnt++;
}
else sel1[i] = 0;
/* check if this atom is in the second selection (negative means all species) */
if (specieID2 < 0 || specie[index] == specieID2)
{
sel2[i] = 1;
sel2cnt++;
}
else sel2[i] = 0;
/* count the number of atoms that are in both selections */
if (sel1[i] && sel2[i]) duplicates++;
}
/* compute the histogram for the RDF */
status = computeHistogram(numAtoms, numVisible, visibleAtoms, pos, pbc, cellDims,
sel1, sel2, start, finish, interval, rdf);
/* free memory used for selections */
free(sel1);
free(sel2);
/* return if there was an error */
if (status) return NULL;
/* normalise the rdf */
normaliseRDF(numBins, sel1cnt, sel2cnt, duplicates, start, interval, cellDims, rdf);
/* return None */
Py_INCREF(Py_None);
return Py_None;
}
/*******************************************************************************
** Calculate the bond order parameters and filter atoms (if required).
**
** Inputs:
** - visibleAtoms: the list of atoms that are currently visible
** - pos: positions of all the atoms
** - maxBondDistance: the maximum bond distance to consider
** - scalarsQ4: array to store the Q4 parameter value
** - scalarsQ6: array to store the Q6 parameter value
** - cellDims: simulation cell dimensions
** - PBC: periodic boundaries conditions
** - NScalars: the number of previously calculated scalar values
** - fullScalars: the full list of previously calculated scalars
** - NVectors: the number of previously calculated vector values
** - fullVectors: the full list of previously calculated vectors
** - filterQ4: filter atoms by the Q4 parameter
** - minQ4: the minimum Q4 for an atom to be visible
** - maxQ4: the maximum Q4 for an atom to be visible
** - filterQ6: filter atoms by the Q6 parameter
** - minQ6: the minimum Q6 for an atom to be visible
** - maxQ6: the maximum Q6 for an atom to be visible
*******************************************************************************/
static PyObject*
bondOrderFilter(PyObject *self, PyObject *args)
{
int NVisibleIn, *visibleAtoms, *PBC, NScalars, filterQ4Enabled, filterQ6Enabled;
int NVectors;
double maxBondDistance, *scalarsQ4, *scalarsQ6, *cellDims;
double *pos, *fullScalars, minQ4, maxQ4, minQ6, maxQ6;
PyArrayObject *posIn=NULL;
PyArrayObject *visibleAtomsIn=NULL;
PyArrayObject *PBCIn=NULL;
PyArrayObject *scalarsQ4In=NULL;
PyArrayObject *scalarsQ6In=NULL;
PyArrayObject *cellDimsIn=NULL;
PyArrayObject *fullScalarsIn=NULL;
PyArrayObject *fullVectors=NULL;
int i, NVisible, boxstat;
double *visiblePos, maxSep2;
struct Boxes *boxes;
struct NeighbourList *nebList;
struct AtomStructureResults *results;
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "O!O!dO!O!O!O!iO!iddiddiO!", &PyArray_Type, &visibleAtomsIn, &PyArray_Type, &posIn, &maxBondDistance,
&PyArray_Type, &scalarsQ4In, &PyArray_Type, &scalarsQ6In, &PyArray_Type, &cellDimsIn, &PyArray_Type, &PBCIn, &NScalars,
&PyArray_Type, &fullScalarsIn, &filterQ4Enabled, &minQ4, &maxQ4, &filterQ6Enabled, &minQ6, &maxQ6, &NVectors,
&PyArray_Type, &fullVectors))
return NULL;
if (not_intVector(visibleAtomsIn)) return NULL;
visibleAtoms = pyvector_to_Cptr_int(visibleAtomsIn);
NVisibleIn = (int) PyArray_DIM(visibleAtomsIn, 0);
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
if (not_doubleVector(scalarsQ4In)) return NULL;
scalarsQ4 = pyvector_to_Cptr_double(scalarsQ4In);
if (not_doubleVector(scalarsQ6In)) return NULL;
scalarsQ6 = pyvector_to_Cptr_double(scalarsQ6In);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
if (not_intVector(PBCIn)) return NULL;
PBC = pyvector_to_Cptr_int(PBCIn);
if (not_doubleVector(fullScalarsIn)) return NULL;
fullScalars = pyvector_to_Cptr_double(fullScalarsIn);
if (not_doubleVector(fullVectors)) return NULL;
/* construct array of positions of visible atoms */
visiblePos = malloc(3 * NVisibleIn * sizeof(double));
if (visiblePos == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate visiblePos");
return NULL;
}
for (i = 0; i < NVisibleIn; i++)
{
int index = visibleAtoms[i];
int ind3 = 3 * index;
int i3 = 3 * i;
visiblePos[i3 ] = pos[ind3 ];
visiblePos[i3 + 1] = pos[ind3 + 1];
visiblePos[i3 + 2] = pos[ind3 + 2];
}
/* box visible atoms */
boxes = setupBoxes(maxBondDistance, PBC, cellDims);
if (boxes == NULL)
{
free(visiblePos);
return NULL;
}
boxstat = putAtomsInBoxes(NVisibleIn, visiblePos, boxes);
if (boxstat)
{
free(visiblePos);
return NULL;
}
/* build neighbour list */
maxSep2 = maxBondDistance * maxBondDistance;
nebList = constructNeighbourList(NVisibleIn, visiblePos, boxes, cellDims, PBC, maxSep2);
/* only required for building neb list */
free(visiblePos);
freeBoxes(boxes);
/* return if failed to build the neighbour list */
if (nebList == NULL) return NULL;
/* allocate results structure */
results = malloc(NVisibleIn * sizeof(struct AtomStructureResults));
if (results == NULL)
{
PyErr_SetString(PyExc_MemoryError, "Could not allocate results");
freeNeighbourList(nebList, NVisibleIn);
return NULL;
}
/* first calc q_lm for each atom over all m values */
complex_qlm(NVisibleIn, visibleAtoms, nebList, pos, cellDims, PBC, results);
/* free neighbour list */
freeNeighbourList(nebList, NVisibleIn);
/* calculate Q4 and Q6 */
calculate_Q(NVisibleIn, results);
/* do filtering here, storing results along the way */
NVisible = 0;
for (i = 0; i < NVisibleIn; i++)
{
int j;
double q4 = results[i].Q4;
double q6 = results[i].Q6;
/* skip if not within the valid range */
if (filterQ4Enabled && (q4 < minQ4 || q4 > maxQ4))
continue;
if (filterQ6Enabled && (q6 < minQ6 || q6 > maxQ6))
continue;
/* store in visible atoms array */
visibleAtoms[NVisible] = visibleAtoms[i];
/* store calculated values */
scalarsQ4[NVisible] = q4;
scalarsQ6[NVisible] = q6;
/* update full scalars/vectors arrays */
for (j = 0; j < NScalars; j++)
{
int nj = j * NVisibleIn;
fullScalars[nj + NVisible] = fullScalars[nj + i];
}
for (j = 0; j < NVectors; j++)
{
int nj = j * NVisibleIn;
DIND2(fullVectors, nj + NVisible, 0) = DIND2(fullVectors, nj + i, 0);
DIND2(fullVectors, nj + NVisible, 1) = DIND2(fullVectors, nj + i, 1);
DIND2(fullVectors, nj + NVisible, 2) = DIND2(fullVectors, nj + i, 2);
}
NVisible++;
}
/* free results memory */
free(results);
return Py_BuildValue("i", NVisible);
}
/*******************************************************************************
* eliminate pbc flicker
*******************************************************************************/
static PyObject*
eliminatePBCFlicker(PyObject *self, PyObject *args)
{
int NAtoms, *pbc;
double *pos, *previousPos, *cellDims;
PyArrayObject *posIn=NULL;
PyArrayObject *previousPosIn=NULL;
PyArrayObject *cellDimsIn=NULL;
PyArrayObject *pbcIn=NULL;
int i, j, count;
double sep, absSep, halfDims[3];
/* parse and check arguments from Python */
if (!PyArg_ParseTuple(args, "iO!O!O!O!", &NAtoms, &PyArray_Type, &posIn, &PyArray_Type, &previousPosIn,
&PyArray_Type, &cellDimsIn, &PyArray_Type, &pbcIn))
return NULL;
if (not_intVector(pbcIn)) return NULL;
pbc = pyvector_to_Cptr_int(pbcIn);
if (not_doubleVector(posIn)) return NULL;
pos = pyvector_to_Cptr_double(posIn);
if (not_doubleVector(previousPosIn)) return NULL;
previousPos = pyvector_to_Cptr_double(previousPosIn);
if (not_doubleVector(cellDimsIn)) return NULL;
cellDims = pyvector_to_Cptr_double(cellDimsIn);
/* half of cellDims */
halfDims[0] = cellDims[0] * 0.5;
halfDims[1] = cellDims[1] * 0.5;
halfDims[2] = cellDims[2] * 0.5;
/* loop over atoms */
count = 0;
for (i = 0; i < NAtoms; i++)
{
sep = atomicSeparation2(pos[3*i], pos[3*i+1], pos[3*i+2], previousPos[3*i], previousPos[3*i+1], previousPos[3*i+2],
cellDims[0], cellDims[1], cellDims[2], pbc[0], pbc[1], pbc[2]);
for (j = 0; j < 3; j++)
{
if (sep < 1.0 && pos[3*i+j] < 1.0)
{
absSep = fabs(pos[3*i+j] - previousPos[3*i+j]);
if (absSep > halfDims[j])
{
pos[3*i+j] += cellDims[j];
count++;
}
}
else if (sep < 1.0 && fabs(cellDims[j] - pos[3*i+j]) < 1.0)
{
absSep = fabs(pos[3*i+j] - previousPos[3*i+j]);
if (absSep > halfDims[j])
{
pos[3*i+j] -= cellDims[j];
count++;
}
}
}
}
return Py_BuildValue("i", count);
}