merge complete
This commit is contained in:
commit
fca61cd47a
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@ -30,24 +30,14 @@ interaction_ufunc_force
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, void * data)
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{
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char * in = args[0]
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, * raw_coefficients = args[1]
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, * out = args[2];
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, * out = args[1];
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npy_intp n = dimensions[0];
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npy_intp in_step = steps[0]
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, raw_coefficients_steps = steps[1]
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, out_step = steps[2];
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, out_step = steps[1];
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npy_intp i;
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// Copy the coefficients to a safe array.
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// This is because NumPy arrays are not
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// necessarily cast-safe.
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float coefficients[19];
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for(i = 0; i < 19; i++)
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{
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coefficients[i] = *(float *)raw_coefficients;
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raw_coefficients += raw_coefficients_steps;
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}
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float * coefficients = (float *) data;
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for(i = 0; i < n; i++)
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{
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@ -73,27 +63,17 @@ interaction_ufunc_float2D
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, * y_old = args[1]
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, * p_x_old = args[2]
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, * p_y_old = args[3]
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, * raw_coefficients = args[4]
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, * p_x_new = args[5]
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, * p_y_new = args[6];
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, * p_x_new = args[4]
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, * p_y_new = args[5];
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npy_intp x_old_steps = steps[0]
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, y_old_steps = steps[1]
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, p_x_old_steps = steps[2]
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, p_y_old_steps = steps[3]
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, raw_coefficients_steps = steps[4]
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, p_x_new_steps = steps[5]
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, p_y_new_steps = steps[6];
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, p_x_new_steps = steps[4]
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, p_y_new_steps = steps[5];
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// Copy the coefficients to a safe array.
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// This is because NumPy arrays are not
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// necessarily cast-safe.
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float coefficients[19];
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for(i = 0; i < 19; i++)
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{
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coefficients[i] = *(float *)raw_coefficients;
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raw_coefficients += raw_coefficients_steps;
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}
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float *coefficients = (float *) data;
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// Compute the new momenta:
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@ -135,30 +115,159 @@ interaction_ufunc_float2D
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// Update the momenta.
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delta_p_x = delta_x_e * interaction_force_function(r, coefficients);
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delta_p_y = delty_y_e * interaction_force_function(r, coefficients);
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*(float *)(p_x_new + i*p_x_new_steps) -= delta_p_x;
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*(float *)(p_y_new + i*p_y_new_steps) -= delta_p_y;
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*(float *)(p_x_new + j*p_x_new_steps) += delta_p_x;
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*(float *)(p_y_new + j*p_y_new_steps) += delta_p_y;
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//printf("%d, %d: %f, %f\n", i, j, delta_p_x, delta_p_y);
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*(float *)(p_x_new + i*p_x_new_steps) += delta_p_x;
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*(float *)(p_y_new + i*p_y_new_steps) += delta_p_y;
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*(float *)(p_x_new + j*p_x_new_steps) -= delta_p_x;
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*(float *)(p_y_new + j*p_y_new_steps) -= delta_p_y;
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}
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}
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}
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static char interaction_types[] =
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{ NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT};
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static char force_types[] =
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{ NPY_FLOAT, NPY_FLOAT};
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static PyUFuncGenericFunction force_funcs[1] =
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{ interaction_ufunc_force};
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static PyUFuncGenericFunction interaction_funcs[1] =
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{ interaction_ufunc_float2D};
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typedef struct
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{
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PyObject_HEAD
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float coefficients[19];
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PyObject * ufunc;
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void *data[1];
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} interaction_UFuncWrapper;
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static int
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interaction_UFuncWrapper_init
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( interaction_UFuncWrapper * self
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, PyObject * args
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, PyObject * kwds)
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{
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// 0: ufunc_force
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// 1: interaction2D
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char type;
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PyObject * coefficients;
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int i;
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PyObject * this_coefficient;
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char *kwords[] = { "type_", "coefficients", NULL};
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if(!PyArg_ParseTupleAndKeywords(args, kwds, "bO", kwords, &type, &coefficients))
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{
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return -1;
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}
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if(!PySequence_Check(coefficients))
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{
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return -1;
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}
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if(PySequence_Size(coefficients) != 19)
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{
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PyErr_SetString(PyExc_ValueError, "coefficients must have length 19");
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return -1;
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}
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// copy the coefficients.
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for(i = 0; i < 19; i++)
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{
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this_coefficient = PySequence_GetItem(coefficients, i);
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if(!this_coefficient)
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{
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return -1;
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}
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// XXX: PyFloat_AsDouble might call python code,
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// so make sure that nothing bad can happen.
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Py_INCREF(this_coefficient);
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self->coefficients[i] = PyFloat_AsDouble(this_coefficient);
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Py_DECREF(this_coefficient);
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if(PyErr_Occurred())
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{
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return -1;
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}
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}
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self->data[0] = (void *)self->coefficients;
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switch(type)
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{
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case 0:
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{
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self->ufunc = PyUFunc_FromFuncAndData(
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force_funcs // func
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, self->data // data
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, force_types //types
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, 1 // ntypes
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, 1 // nin
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, 1 // nout
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, PyUFunc_None // identity
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, "force_function" // name
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, "computes the scalar force between two particles with given coefficients" // doc
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, 0); // unused
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break;
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}
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case 1:
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{
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self->ufunc = PyUFunc_FromFuncAndData(
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interaction_funcs
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, self->data
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, interaction_types
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, 1
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, 4
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, 2
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, PyUFunc_None
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, "interaction2D"
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, "Update the momenta according to the given coefficients and positions"
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, 0);
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break;
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}
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default:
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{
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PyErr_SetString(PyExc_ValueError, "unknown ufunc type, must be 0 or 1");
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return -1;
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}
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}
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Py_INCREF(self->ufunc);
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return 0;
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}
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static PyObject *
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interaction_UFuncWrapper_call
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(interaction_UFuncWrapper * self
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, PyObject * args
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, PyObject * kwargs)
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{
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return PyObject_Call(self->ufunc, args, kwargs);
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}
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static PyMemberDef interaction_UFuncWrapper_members[] =
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{
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{"ufunc", T_OBJECT_EX, offsetof(interaction_UFuncWrapper, ufunc), 0, "ufunc"},
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{NULL}
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};
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static PyTypeObject interaction_UFuncWrapperType =
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{
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PyVarObject_HEAD_INIT(NULL, 0)
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.tp_name = "brown.interaction.UFuncWrapper",
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.tp_doc = "A wrapper that wraps the ufuncs for interaction and force, storing the coefficients",
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.tp_basicsize = sizeof(interaction_UFuncWrapper),
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.tp_itemsize = 0,
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.tp_flags = Py_TPFLAGS_DEFAULT,
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.tp_new = PyType_GenericNew,
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.tp_init = (initproc) interaction_UFuncWrapper_init,
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.tp_call = interaction_UFuncWrapper_call,
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.tp_members = interaction_UFuncWrapper_members
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};
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static PyMethodDef InteractionMethods[] = {
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{NULL, NULL, 0, NULL}
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};
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PyUFuncGenericFunction interaction_funcs[] =
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{ &interaction_ufunc_float2D};
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PyUFuncGenericFunction force_funcs[] =
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{ &interaction_ufunc_force};
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static char interaction_types[] =
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{ NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT, NPY_FLOAT};
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static char force_types[] =
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{ NPY_FLOAT, NPY_FLOAT, NPY_FLOAT};
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static void *interaction_data[] = {NULL};
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static void *force_data[] = {NULL};
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static struct PyModuleDef moduledef = {
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PyModuleDef_HEAD_INIT
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@ -175,10 +284,12 @@ static struct PyModuleDef moduledef = {
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PyMODINIT_FUNC
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PyInit_interaction(void)
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{
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PyObject * module
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, * ufunc_interaction
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, * ufunc_force
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, * dct;
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PyObject * module;
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if(PyType_Ready(&interaction_UFuncWrapperType) < 0)
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{
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return NULL;
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}
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module = PyModule_Create(&moduledef);
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if(!module)
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@ -188,36 +299,8 @@ PyInit_interaction(void)
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import_array();
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import_ufunc();
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ufunc_interaction = PyUFunc_FromFuncAndDataAndSignature(
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interaction_funcs
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, interaction_data
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, interaction_types
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, 1
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, 5
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, 2
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, PyUFunc_None
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, "interaction2D"
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, "Update the momenta according to the given coefficients and positions"
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, 0
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, "(n),(n),(n),(n),(19)->(n),(n)");
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ufunc_force = PyUFunc_FromFuncAndDataAndSignature(
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force_funcs
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, force_data
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, force_types
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, 1
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, 2
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, 1
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, PyUFunc_None
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, "force_function"
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, "computes the scalar force between two particles with given coefficients"
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, 0
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, "(n),(19)->(n)");
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dct = PyModule_GetDict(module);
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PyDict_SetItemString(dct, "interaction2D", ufunc_interaction);
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PyDict_SetItemString(dct, "force_function", ufunc_force);
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Py_DECREF(ufunc_interaction);
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Py_DECREF(ufunc_force);
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Py_INCREF(&interaction_UFuncWrapperType);
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PyModule_AddObject(module, "UFuncWrapper", (PyObject *) &interaction_UFuncWrapperType);
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return module;
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}
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|
|
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@ -2,8 +2,12 @@
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#define interaction_h
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#include <Python.h>
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#include "structmember.h"
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// XXX
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#include <numpy/ndarraytypes.h>
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#include <numpy/ufuncobject.h>
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#include <stddef.h>
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/*
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* This is a quite generic force function mapping a
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|
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@ -28,5 +32,11 @@ interaction_ufunc_float2D
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, npy_intp * steps
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, void * data);
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static void
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interaction_ufunc_force
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( char ** args
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, npy_intp * dimensions
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, npy_intp * steps
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, void * data);
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#endif
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|
|
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|
|
@ -0,0 +1,57 @@
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from brown.interaction import UFuncWrapper
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from brown.brown import BrownIterator
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import numpy as np
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from collections import deque
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from copy import copy
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import matplotlib.pyplot as plt
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import matplotlib.animation as ani
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|
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c = np.array([5, 10, 20, 30, 0, 0, 0, 1, -20, 0, -2, -0.1, 2, 0, 0, 0, 0, 0, 0], dtype=np.float16)
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#force_function = UFuncWrapper(0, c)
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#interaction2D = UFuncWrapper(1, c)
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borders_x = [-100, 100]
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borders_y = [-100, 100]
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n_particles = 6
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frames = 1000
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|
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x_coords = np.random.uniform(borders_x[0] / 2, borders_x[1] / 2, n_particles).astype(np.float16)
|
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y_coords = np.random.uniform(borders_y[0] / 2, borders_y[1] / 2, n_particles).astype(np.float16)
|
||||
|
||||
|
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x_momenta = np.zeros(n_particles, dtype=np.float16)
|
||||
y_momenta = np.zeros(n_particles, dtype=np.float16)
|
||||
|
||||
|
||||
|
||||
fig = plt.figure(figsize=(7, 7))
|
||||
ax = fig.add_axes([0, 0, 1, 1], frameon=False)
|
||||
ax.set_xlim(*borders_x)
|
||||
ax.set_xticks([])
|
||||
ax.set_ylim(*borders_y)
|
||||
ax.set_yticks([])
|
||||
|
||||
plot, = ax.plot(x_coords, y_coords, "b.")
|
||||
center_of_mass, = ax.plot(x_coords.mean(), y_coords.mean(), "r-")
|
||||
center_of_mass_history_x = deque([x_coords.mean()])
|
||||
center_of_mass_history_y = deque([y_coords.mean()])
|
||||
|
||||
brown = BrownIterator(-1, c
|
||||
, x_coords, y_coords
|
||||
, y_momenta, y_momenta
|
||||
, borders_x, borders_y
|
||||
, border_dampening=1
|
||||
, dt=0.001)
|
||||
|
||||
u = iter(brown)
|
||||
|
||||
def update(i):
|
||||
data = next(u)
|
||||
center_of_mass_history_x.append(x_coords.mean())
|
||||
center_of_mass_history_y.append(y_coords.mean())
|
||||
|
||||
plot.set_data(*data)
|
||||
center_of_mass.set_data(center_of_mass_history_x, center_of_mass_history_y)
|
||||
|
||||
animation = ani.FuncAnimation(fig, update, range(frames), interval=1)
|
||||
plt.show()
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
from brown.interaction import UFuncWrapper
|
||||
import numpy as np
|
||||
|
||||
class BrownIterator(object):
|
||||
def __init__(self
|
||||
, m
|
||||
, c
|
||||
, x
|
||||
, y
|
||||
, px
|
||||
, py
|
||||
, borders_x
|
||||
, borders_y
|
||||
, speed_of_light=1e3 # The value that will replace NaN momenta
|
||||
, border_dampening=1
|
||||
, dt=0.1):
|
||||
self._max_m = m
|
||||
self._i = 0
|
||||
self.c = c
|
||||
self.x = x
|
||||
self.y = y
|
||||
self.px = px
|
||||
self.py = py
|
||||
self.borders_x = borders_x
|
||||
self.borders_y = borders_y
|
||||
self.dt = dt
|
||||
self.speed_of_light = speed_of_light
|
||||
self.border_dampening = border_dampening
|
||||
self._interaction = UFuncWrapper(1, c)
|
||||
def __iter__(self):
|
||||
self._i = 0
|
||||
return self
|
||||
def __next__(self):
|
||||
self._i += 1
|
||||
if(self._i > self._max_m and self._max_m > 0):
|
||||
raise StopIteration()
|
||||
if(self._i == 1):
|
||||
return self.x, self.y
|
||||
|
||||
self.px, self.py = self._interaction(self.x, self.y, self.px, self.py)
|
||||
self.px[np.isnan(self.px)] = self.speed_of_light
|
||||
self.py[np.isnan(self.py)] = self.speed_of_light
|
||||
self._reflect_at_borders()
|
||||
|
||||
self.x += self.dt * self.px
|
||||
self.y += self.dt * self.py
|
||||
|
||||
return self.x, self.y
|
||||
|
||||
|
||||
def _reflect_at_borders(self):
|
||||
if(len(self.borders_x) > 0):
|
||||
self.px[self.x <= self.borders_x[0]] *= -self.border_dampening
|
||||
self.x[self.x <= self.borders_x[0]] = self.borders_x[0]
|
||||
if(len(self.borders_x) > 1):
|
||||
self.px[self.x >= self.borders_x[1]] *= -self.border_dampening
|
||||
self.x[self.x >= self.borders_x[1]] = self.borders_x[1]
|
||||
if(len(self.borders_y) > 0):
|
||||
self.py[self.y <= self.borders_y[0]] *= -self.border_dampening
|
||||
self.y[self.y <= self.borders_y[0]] = self.borders_y[0]
|
||||
if(len(self.borders_y) > 1):
|
||||
self.py[self.y >= self.borders_y[1]] *= -self.border_dampening
|
||||
self.y[self.y >= self.borders_y[1]] = self.borders_y[1]
|
||||
|
||||
|
||||
|
||||
55
setup.py
55
setup.py
|
|
@ -1,30 +1,31 @@
|
|||
#from distutils.core import setup, Extension
|
||||
#
|
||||
#
|
||||
#interaction = Extension("brown.interaction",
|
||||
# sources = ["c/interaction/interaction.c"])
|
||||
#
|
||||
#setup(name = "brown",
|
||||
# version = "0.0.1",
|
||||
# description = "Me playing around with single-atom classical gases",
|
||||
# ext_modules = [interaction],
|
||||
# packages = [
|
||||
# "brown"
|
||||
# ],
|
||||
# package_dir = {"brown": "py/brown"},
|
||||
# #url="https://github.com/daknuett/python3-nf",
|
||||
# author = "Daniel Knüttel",
|
||||
# author_email = "daniel.knuettel@daknuett.eu")
|
||||
from distutils.core import setup, Extension
|
||||
|
||||
def configuration(parent_package='', top_path=None):
|
||||
from numpy.distutils.misc_util import Configuration
|
||||
|
||||
config = Configuration('brown'
|
||||
, parent_package
|
||||
, top_path)
|
||||
config.add_extension('interaction', ['c/interaction/interaction.c'])
|
||||
return config
|
||||
interaction = Extension("brown.interaction",
|
||||
sources = ["c/interaction/interaction.c"])
|
||||
|
||||
if __name__ == "__main__":
|
||||
from numpy.distutils.core import setup
|
||||
setup(configuration=configuration)
|
||||
setup(name = "brown",
|
||||
version = "0.0.1",
|
||||
description = "Me playing around with single-atom classical gases",
|
||||
ext_modules = [interaction],
|
||||
packages = [
|
||||
"brown"
|
||||
],
|
||||
package_dir = {"brown": "py/brown"},
|
||||
#url="https://github.com/daknuett/python3-nf",
|
||||
author = "Daniel Knüttel",
|
||||
author_email = "daniel.knuettel@daknuett.eu")
|
||||
|
||||
#def configuration(parent_package='', top_path=None):
|
||||
# from numpy.distutils.misc_util import Configuration
|
||||
#
|
||||
# config = Configuration('brown'
|
||||
# , parent_package
|
||||
# , top_path="py/")
|
||||
# config.add_extension('interaction', ['c/interaction/interaction.c'], extra_compile_args=["-g"])
|
||||
# #config.add_subpackage("brown.brown", "py/brown")
|
||||
# return config
|
||||
#
|
||||
#if __name__ == "__main__":
|
||||
# from numpy.distutils.core import setup
|
||||
# setup(configuration=configuration)
|
||||
|
|
|
|||
72
test.py
72
test.py
|
|
@ -1,46 +1,50 @@
|
|||
from brown.interaction import interaction2D,force_function
|
||||
from brown.interaction import UFuncWrapper
|
||||
import numpy as np
|
||||
from collections import deque
|
||||
from copy import copy
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
c = np.array([5, 10, 20, 0, 0, 0, 0, 1, -2, 0, -2, -0.1, 2, 0, 0, 0, 0, 0, 0], dtype=np.float16)
|
||||
print(c)
|
||||
c = np.array([5, 10, 20, 30, 0, 0, 0, 1, -20, 0, -2, -0.1, 2, 0, 0, 0, 0, 0, 0], dtype=np.float16)
|
||||
force_function = UFuncWrapper(0, c)
|
||||
interaction2D = UFuncWrapper(1, c)
|
||||
|
||||
#x_coords = np.array([0, 1], dtype=np.float16)
|
||||
#y_coords = np.array([0, 0], dtype=np.float16)
|
||||
#
|
||||
#x_momenta = np.array([0, 0], dtype=np.float16)
|
||||
#y_momenta = np.array([0, 0], dtype=np.float16)
|
||||
#
|
||||
#time = np.arange(0, 5, 1, dtype=np.float16)
|
||||
#
|
||||
#time_evolution = deque()
|
||||
#
|
||||
#for t in time:
|
||||
# x_momenta, y_momenta = interaction2D(x_coords, y_coords, x_momenta, y_momenta, c)
|
||||
# x_coords += x_momenta
|
||||
# y_coords += y_momenta
|
||||
#
|
||||
# time_evolution.append(copy(x_coords))
|
||||
#
|
||||
#time_evolution = np.array(time_evolution)
|
||||
#
|
||||
#particle_one_evolution = time_evolution[:, 0]
|
||||
#particle_two_evolution = time_evolution[:, 1]
|
||||
x_coords = np.array([0, 1], dtype=np.float16)
|
||||
y_coords = np.array([0, 0], dtype=np.float16)
|
||||
|
||||
#plt.subplot(2, 1, 1)
|
||||
r = np.arange(0, 0.5, 0.01, dtype=np.float16)
|
||||
x_momenta = np.array([0, 0], dtype=np.float16)
|
||||
y_momenta = np.array([0, 0], dtype=np.float16)
|
||||
|
||||
time = np.arange(0, 50, 1, dtype=np.float16)
|
||||
|
||||
time_evolution = deque()
|
||||
|
||||
dt = 0.1
|
||||
|
||||
for t in time:
|
||||
x_momenta, y_momenta = interaction2D(x_coords, y_coords, x_momenta, y_momenta)
|
||||
x_coords += dt * x_momenta
|
||||
y_coords += dt * y_momenta
|
||||
|
||||
time_evolution.append(copy(x_coords))
|
||||
|
||||
time_evolution = np.array(time_evolution)
|
||||
|
||||
particle_one_evolution = time_evolution[:, 0]
|
||||
particle_two_evolution = time_evolution[:, 1]
|
||||
|
||||
plt.subplot(2, 1, 1)
|
||||
|
||||
r = np.arange(0, 50, 0.1, dtype=np.float16)
|
||||
plt.title("Force")
|
||||
plt.xlabel("particle distance")
|
||||
plt.ylabel("scalar force")
|
||||
plt.plot(r, force_function(r, c))
|
||||
plt.plot(r, force_function(r))
|
||||
|
||||
#plt.subplot(2, 1, 2)
|
||||
#plt.title("Particle x-positions over time")
|
||||
#plt.xlabel("time")
|
||||
#plt.ylabel("particle x-position")
|
||||
#h0, = plt.plot(time, particle_one_evolution, label="particle 1")
|
||||
#h1, = plt.plot(time, particle_two_evolution, label="particle 2")
|
||||
#plt.legend(handles=[h0, h1])
|
||||
plt.subplot(2, 1, 2)
|
||||
plt.title("Particle x-positions over time")
|
||||
plt.xlabel("time")
|
||||
plt.ylabel("particle x-position")
|
||||
h0, = plt.plot(time, particle_one_evolution, label="particle 1")
|
||||
h1, = plt.plot(time, particle_two_evolution, label="particle 2")
|
||||
plt.legend(handles=[h0, h1])
|
||||
plt.show()
|
||||
|
|
|
|||
Loading…
Reference in New Issue