static PyObject* Py_convert_shape(
PyObject* self,
PyObject* args)
{
PyObject* landmarks_obj;
int format;
if (!PyArg_ParseTuple(args, "Oi:convert_shape", &landmarks_obj, &format))
return NULL;
PyArrayObject* landmarks_array = (PyArrayObject*)
PyArray_FROM_OTF(landmarks_obj, NPY_FLOAT, NPY_ARRAY_IN_ARRAY);
if (landmarks_array == NULL)
{
PyErr_SetString(PyExc_TypeError, landmark_error);
return NULL;
}
if (PyArray_NDIM(landmarks_array) != 2)
{
PyErr_SetString(PyExc_TypeError, landmark_dim_error);
return NULL;
}
PyObject* retArray = PyArray_Copy(landmarks_array);
Py_DECREF(landmarks_array);
float* landmarks = (float*)PyArray_DATA((PyArrayObject*)retArray);
stasm_convert_shape(landmarks, format);
return retArray;
}
/* optimize float array or complex array to a scalar power */
static PyObject *
fast_scalar_power(PyArrayObject *a1, PyObject *o2, int inplace)
{
double exp;
if (PyArray_Check(a1) && array_power_is_scalar(o2, &exp)) {
PyObject *fastop = NULL;
if (PyArray_ISFLOAT(a1) || PyArray_ISCOMPLEX(a1)) {
if (exp == 1.0) {
/* we have to do this one special, as the
"copy" method of array objects isn't set
up early enough to be added
by PyArray_SetNumericOps.
*/
if (inplace) {
Py_INCREF(a1);
return (PyObject *)a1;
} else {
return PyArray_Copy(a1);
}
}
else if (exp == -1.0) {
fastop = n_ops.reciprocal;
}
else if (exp == 0.0) {
fastop = n_ops.ones_like;
}
else if (exp == 0.5) {
fastop = n_ops.sqrt;
}
else if (exp == 2.0) {
fastop = n_ops.square;
}
else {
return NULL;
}
if (inplace) {
return PyArray_GenericInplaceUnaryFunction(a1, fastop);
} else {
return PyArray_GenericUnaryFunction(a1, fastop);
}
}
else if (exp==2.0) {
fastop = n_ops.multiply;
if (inplace) {
return PyArray_GenericInplaceBinaryFunction
(a1, (PyObject *)a1, fastop);
}
else {
return PyArray_GenericBinaryFunction
(a1, (PyObject *)a1, fastop);
}
}
}
return NULL;
}
PyObject*
sndarray_array (PyObject* self, PyObject* arg)
{
PyObject *array, *arraycopy=NULL;
/*we'll let numeric do the copying for us*/
array = sndarray_samples (self, arg);
if(array)
{
arraycopy = PyArray_Copy ((PyArrayObject*) array);
Py_DECREF (array);
}
return arraycopy;
}
static PyObject* Py_force_points_into_image(
PyObject* self,
PyObject* args)
{
PyObject* landmarks_obj;
PyObject* img_obj;
if (!PyArg_ParseTuple(args, "OO:force_points_into_image",
&landmarks_obj, &img_obj))
return NULL;
PyArrayObject* landmarks_array = (PyArrayObject*)
PyArray_FROM_OTF(landmarks_obj, NPY_FLOAT, NPY_ARRAY_IN_ARRAY);
if (landmarks_array == NULL)
{
PyErr_SetString(PyExc_TypeError, landmark_error);
return NULL;
}
if (PyArray_NDIM(landmarks_array) != 2)
{
PyErr_SetString(PyExc_TypeError, landmark_dim_error);
return NULL;
}
int width, height;
if (PyArray_to_image(img_obj, &width, &height) == NULL)
return NULL;
PyObject* retArray = PyArray_Copy(landmarks_array);
Py_DECREF(landmarks_array);
float* landmarks = (float*)PyArray_DATA((PyArrayObject*)retArray);
stasm_force_points_into_image(landmarks, width, height);
return retArray;
}
// * GCHMCIntegrator Constructor * //
GCHMCIntegrator::GCHMCIntegrator(PyObject *universe, std::string ligdir, std::string gaff_fn)
{
std::cout<<"GCHMCIntegrator instance created 20160826"<<std::endl;
import_array();
temperature = 300.0;
delta_t = 0.0015;
trouble = 0;
this->universe = universe;
PyObject *pyo_universe_spec;
pyo_universe_spec = PyObject_GetAttrString(universe, "_spec");
universe_spec = (PyUniverseSpecObject *)pyo_universe_spec;
PyObject *objectList;
objectList = PyObject_CallMethod(universe, "objectList", NULL);
PyObject *object0 = PyList_GetItem(objectList, 0);
// * Get confarr * //
PyObject *confobj;
PyObject *confarr;
confobj = PyObject_CallMethod(universe, "configuration", NULL);
confarr = PyObject_GetAttrString(confobj, "array");
configuration = (PyArrayObject *)confarr;
vector3 *x;
x = (vector3 *)configuration->data;
p_energy_po = new energy_data;
#if defined(NUMPY)
gradarr = (PyArrayObject *)PyArray_Copy(configuration);
#else
gradarr = (PyArrayObject *)PyArray_FromDims(configuration->nd, configuration->dimensions, PyArray_DOUBLE);
#endif
vector3 *f;
f = (vector3 *)gradarr->data;
for(int i=0; i<configuration->dimensions[0]; i++){
f[i][0] = f[i][1] = f[i][2] = .0;
}
p_energy_po->gradients = (PyObject *)gradarr;
p_energy_po->gradient_fn = NULL;
p_energy_po->force_constants = NULL;
p_energy_po->fc_fn = NULL;
int natoms = configuration->dimensions[0];
int order[natoms+2];
int acceptance;
PyObject *prmtop_order_obj = PyObject_GetAttrString(object0, "prmtop_order");
for(int i=0; i<PyList_Size(prmtop_order_obj); i++){
order[i] = (int)PyInt_AS_LONG( PyObject_GetAttrString(PyList_GetItem((prmtop_order_obj), i), "number") );
}
PyArrayObject *prmtop_order = (PyArrayObject *)prmtop_order_obj;
order[natoms] = 1;
order[natoms+1] = 1945;
acceptance = order[natoms];
int argc = 6;
ligdir += '/';
//gaffdir += '/';
//string gaff_fn = gaffdir + "gaff.dat";
/* Options are:
IC: Internal Coordinates: fully flexible
TD: Torsional Dynamics: only torsions are flexible
RR: Rigid Rings: torsional dynamics with rigid rings
*/
const char *argv[6] = {
"-ligdir", ligdir.c_str(),
"-gaff", gaff_fn.c_str(),
"-ictd", "TD"
};
//+++++++ Simbody PART ++++++++++++
bArgParser parser(argc, argv);
parser.Print();
TARGET_TYPE **indexMap = NULL;
TARGET_TYPE *PrmToAx_po = NULL;
TARGET_TYPE *MMTkToPrm_po = NULL;
std::cout<<"MMTK configuration->dimensions[0]"<<configuration->dimensions[0]<<std::endl<<std::flush;
indexMap = new TARGET_TYPE*[(configuration->dimensions[0])];
int _indexMap[natoms][3];
PrmToAx_po = new TARGET_TYPE[configuration->dimensions[0]];
MMTkToPrm_po = new TARGET_TYPE[configuration->dimensions[0]];
int natoms3 = 3*(configuration->dimensions[0]);
int arrays_cut = 2 + 4*natoms3;
SHMSZ = (
2*sizeof(TARGET_TYPE) + // Counter and flag
natoms3*sizeof(TARGET_TYPE) + // Positions
natoms3*sizeof(TARGET_TYPE) + // Velocities
natoms3*sizeof(TARGET_TYPE) + // indexMap
natoms3*sizeof(TARGET_TYPE) + // Gradients
5*sizeof(TARGET_TYPE) + // ac + 0 -> 4 // step, nosteps, temperature, timestep, trouble
1*sizeof(TARGET_TYPE) + // ac + 5 // potential energy
2*sizeof(TARGET_TYPE) + // ac + 6->7 // DAE step done; Move accepted
1*sizeof(TARGET_TYPE) + // ac + 8 // KE
1*sizeof(TARGET_TYPE) + // ac + 9 // steps_per_trial
1*sizeof(TARGET_TYPE) //+ // ac + 10 // trial
);
shm = new TARGET_TYPE[SHMSZ];
std::cout<<"parser.mol2F "<<parser.mol2F<<std::endl<<std::flush;
std::cout<<"parser.rbF "<<parser.rbF<<std::endl<<std::flush;
std::cout<<"parser.gaffF "<<parser.gaffF<<std::endl<<std::flush;
std::cout<<"parser.frcmodF "<<parser.frcmodF<<std::endl<<std::flush;
std::cout<<"parser.ictdF "<<parser.ictdF<<std::endl<<std::flush;
// LS EU
//(((PyFFEnergyTermObject **)(evaluator)->terms->data)[5])->param[0] = 0.5;
// LS EU
sys = new SymSystem(
parser.mol2F, parser.rbF, parser.gaffF, parser.frcmodF,
parser.ictdF,
PrmToAx_po, MMTkToPrm_po,
evaluator,
p_energy_po,
configuration,
universe_spec,
shm
);
for(int i=0; i<natoms; i++){
_indexMap[i][2] = order[i];
}
// * Memory alloc for convinient arrays * //
coords = new TARGET_TYPE*[sys->mr->natms];
TARGET_TYPE **vels = new TARGET_TYPE*[sys->mr->natms];
TARGET_TYPE **inivels = new TARGET_TYPE*[sys->mr->natms];
TARGET_TYPE **grads = new TARGET_TYPE*[sys->mr->natms];
// * Seed the random number generator * //
srand (time(NULL));
//+++++++ SERVER PART +++++++++
float mysweep = 0;
shm[0] = CNT_START;
int cli;
sweep = 0;
bool system_initialized = false;
int big_loop_i;
shm[1] = CLIENT_FLAG;
int a;
int start, start_1, stop;
int i = natoms*2*3 + 2;
// * Assign convenient pointers for order * /
start = 2 + natoms3 + natoms3;
for(a=0; a<natoms; a++){
indexMap[a] = &(shm[a*3 + start]);
}
// * Assign order in shm[][2] * //
start = 2 + natoms3 + natoms3;
cli = start;
for (a=0; a<natoms; a++){ // Order
cli += 2;
shm[cli++] = order[a];
}
cli = 2;
for (a=0; a<natoms; a++){ // Positions
shm[cli++] = x[a][0]; shm[cli++] = x[a][1]; shm[cli++] = x[a][2];
}
for (a=0; a<natoms; a++){ // Velocities
shm[cli++] = .0; //vels[a][0];//shm[cli++] = v[a][0];
shm[cli++] = .0; //vels[a][1];//shm[cli++] = v[a][1];
shm[cli++] = .0; //vels[a][2];//shm[cli++] = v[a][2];
}
for (a=0; a<natoms; a++){ // Order
cli += 2;
shm[cli++] = order[a];
}
for (a=0; a<natoms; a++){ // Forces
shm[cli++] = .0; shm[cli++] = .0; shm[cli++] = .0;
}
shm[cli++] = big_loop_i; // Step
shm[cli++] = 50.0; //(TARGET_TYPE)nosteps; // Number of steps
shm[cli++] = temperature; // Temeperature
shm[cli++] = delta_t;
shm[cli++] = trouble;
shm[cli++] = p_energy_po->energy;
cli++; // DAE set only by the server
shm[cli] = acceptance + 0.0;
//Set the client flag
shm[1] = CLIENT_FLAG;
shm[arrays_cut + 6] = 13.0; // set DAE to done
// * Assign convenient pointers for coordinates * //
int shm_coords_sup = (natoms3)+2;
int j=-1, k=0;
start = 2;
for(j=0; j<natoms; j++){
coords[j] = &(shm[j*3 + start]);
}
mysweep = shm[0] - CNT_START;
// * Assign convenient pointers for velocities * //
start = 2 + natoms3;
start_1 = start - 1;
stop = 2 + natoms3 + natoms3;
for(j=0; j<natoms; j++){
vels[j] = &(shm[j*3 + start]);
inivels[j] = &(shm[j*3 + start]);
}
// * Assign convenient pointers for gradients * //
start = 2 + natoms3 + natoms3 + natoms3;
start_1 = start - 1;
stop = 2 + natoms3 + natoms3 + natoms3 + natoms3;
for(j=0; j<natoms; j++){
grads[j] = &(shm[j*3 + start]);
}
// * Rewrite indexMap to memory * /
start = 2 + natoms3 + natoms3;
start_1 = start - 1;
stop = 2 + natoms3 + natoms3 + natoms3;
// ************************* /
// * Initialize Simulation * /
// ************************* /
TARGET_TYPE timestep, mytimestep;
mytimestep = shm[arrays_cut + 3];
// * Build bMainResidue and fill indexMap * /
sys->InitSimulation(coords, vels, inivels, indexMap, grads, mytimestep, true);
system_initialized = true;
}
static PyObject *
_array_copy_nice(PyArrayObject *self)
{
return PyArray_Return((PyArrayObject *) PyArray_Copy(self));
}
/* optimize float array or complex array to a scalar power */
static PyObject *
fast_scalar_power(PyArrayObject *a1, PyObject *o2, int inplace)
{
double exponent;
NPY_SCALARKIND kind; /* NPY_NOSCALAR is not scalar */
if (PyArray_Check(a1) && ((kind=is_scalar_with_conversion(o2, &exponent))>0)) {
PyObject *fastop = NULL;
if (PyArray_ISFLOAT(a1) || PyArray_ISCOMPLEX(a1)) {
if (exponent == 1.0) {
/* we have to do this one special, as the
"copy" method of array objects isn't set
up early enough to be added
by PyArray_SetNumericOps.
*/
if (inplace) {
Py_INCREF(a1);
return (PyObject *)a1;
} else {
return PyArray_Copy(a1);
}
}
else if (exponent == -1.0) {
fastop = n_ops.reciprocal;
}
else if (exponent == 0.0) {
fastop = n_ops._ones_like;
}
else if (exponent == 0.5) {
fastop = n_ops.sqrt;
}
else if (exponent == 2.0) {
fastop = n_ops.square;
}
else {
return NULL;
}
if (inplace) {
return PyArray_GenericInplaceUnaryFunction(a1, fastop);
} else {
return PyArray_GenericUnaryFunction(a1, fastop);
}
}
/* Because this is called with all arrays, we need to
* change the output if the kind of the scalar is different
* than that of the input and inplace is not on ---
* (thus, the input should be up-cast)
*/
else if (exponent == 2.0) {
fastop = n_ops.multiply;
if (inplace) {
return PyArray_GenericInplaceBinaryFunction
(a1, (PyObject *)a1, fastop);
}
else {
PyArray_Descr *dtype = NULL;
PyObject *res;
/* We only special-case the FLOAT_SCALAR and integer types */
if (kind == NPY_FLOAT_SCALAR && PyArray_ISINTEGER(a1)) {
dtype = PyArray_DescrFromType(NPY_DOUBLE);
a1 = (PyArrayObject *)PyArray_CastToType(a1, dtype,
PyArray_ISFORTRAN(a1));
if (a1 == NULL) {
return NULL;
}
}
else {
Py_INCREF(a1);
}
res = PyArray_GenericBinaryFunction(a1, (PyObject *)a1, fastop);
Py_DECREF(a1);
return res;
}
}
}
return NULL;
}
/*NUMPY_API
* Round
*/
NPY_NO_EXPORT PyObject *
PyArray_Round(PyArrayObject *a, int decimals, PyArrayObject *out)
{
PyObject *f, *ret = NULL, *tmp, *op1, *op2;
int ret_int=0;
PyArray_Descr *my_descr;
if (out && (PyArray_SIZE(out) != PyArray_SIZE(a))) {
PyErr_SetString(PyExc_ValueError,
"invalid output shape");
return NULL;
}
if (PyArray_ISCOMPLEX(a)) {
PyObject *part;
PyObject *round_part;
PyObject *arr;
int res;
if (out) {
arr = (PyObject *)out;
Py_INCREF(arr);
}
else {
arr = PyArray_Copy(a);
if (arr == NULL) {
return NULL;
}
}
/* arr.real = a.real.round(decimals) */
part = PyObject_GetAttrString((PyObject *)a, "real");
if (part == NULL) {
Py_DECREF(arr);
return NULL;
}
part = PyArray_EnsureAnyArray(part);
round_part = PyArray_Round((PyArrayObject *)part,
decimals, NULL);
Py_DECREF(part);
if (round_part == NULL) {
Py_DECREF(arr);
return NULL;
}
res = PyObject_SetAttrString(arr, "real", round_part);
Py_DECREF(round_part);
if (res < 0) {
Py_DECREF(arr);
return NULL;
}
/* arr.imag = a.imag.round(decimals) */
part = PyObject_GetAttrString((PyObject *)a, "imag");
if (part == NULL) {
Py_DECREF(arr);
return NULL;
}
part = PyArray_EnsureAnyArray(part);
round_part = PyArray_Round((PyArrayObject *)part,
decimals, NULL);
Py_DECREF(part);
if (round_part == NULL) {
Py_DECREF(arr);
return NULL;
}
res = PyObject_SetAttrString(arr, "imag", round_part);
Py_DECREF(round_part);
if (res < 0) {
Py_DECREF(arr);
return NULL;
}
return arr;
}
/* do the most common case first */
if (decimals >= 0) {
if (PyArray_ISINTEGER(a)) {
if (out) {
if (PyArray_AssignArray(out, a,
NULL, NPY_DEFAULT_ASSIGN_CASTING) < 0) {
return NULL;
}
Py_INCREF(out);
return (PyObject *)out;
}
else {
Py_INCREF(a);
return (PyObject *)a;
}
}
if (decimals == 0) {
if (out) {
return PyObject_CallFunction(n_ops.rint, "OO", a, out);
}
return PyObject_CallFunction(n_ops.rint, "O", a);
}
op1 = n_ops.multiply;
op2 = n_ops.true_divide;
}
else {
op1 = n_ops.true_divide;
op2 = n_ops.multiply;
decimals = -decimals;
}
if (!out) {
if (PyArray_ISINTEGER(a)) {
ret_int = 1;
my_descr = PyArray_DescrFromType(NPY_DOUBLE);
}
else {
Py_INCREF(PyArray_DESCR(a));
my_descr = PyArray_DESCR(a);
}
out = (PyArrayObject *)PyArray_Empty(PyArray_NDIM(a), PyArray_DIMS(a),
my_descr,
PyArray_ISFORTRAN(a));
if (out == NULL) {
return NULL;
}
}
else {
Py_INCREF(out);
}
f = PyFloat_FromDouble(power_of_ten(decimals));
if (f == NULL) {
return NULL;
}
ret = PyObject_CallFunction(op1, "OOO", a, f, out);
if (ret == NULL) {
goto finish;
}
tmp = PyObject_CallFunction(n_ops.rint, "OO", ret, ret);
if (tmp == NULL) {
Py_DECREF(ret);
ret = NULL;
goto finish;
}
Py_DECREF(tmp);
tmp = PyObject_CallFunction(op2, "OOO", ret, f, ret);
if (tmp == NULL) {
Py_DECREF(ret);
ret = NULL;
goto finish;
}
Py_DECREF(tmp);
finish:
Py_DECREF(f);
Py_DECREF(out);
if (ret_int) {
Py_INCREF(PyArray_DESCR(a));
tmp = PyArray_CastToType((PyArrayObject *)ret,
PyArray_DESCR(a), PyArray_ISFORTRAN(a));
Py_DECREF(ret);
return tmp;
}
return ret;
}