def __init__(self, state, size=0, v0=None):
self._state = state
self._V0 = data.ParticleDat(self._state.npart_local, 3, name='v0')
self._VT = state.velocities
self._VO_SET = False
if v0 is not None:
self.set_v0(v0)
else:
self.set_v0(state=self._state)
self._VAF = data.ScalarArray(ncomp=1)
self._V = []
self._T = []
_headers = ['stdio.h']
_constants = None
_kernel_code = '''
VAF(0) += (v0(0)*VT(0) + v0(1)*VT(1) + v0(2)*VT(2))*Ni;
'''
_reduction = (kernel.Reduction('VAF', 'VAF[I]', '+'), )
_static_args = {'Ni': ctypes.c_double}
_kernel = kernel.Kernel('VelocityAutocorrelation', _kernel_code,
_constants, _headers, _reduction, _static_args)
self._datdict = {'VAF': self._VAF, 'v0': self._V0, 'VT': self._VT}
self._loop = loop.ParticleLoop(self._state.as_func('npart_local'),
None,
kernel=_kernel,
dat_dict=self._datdict)
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
OUTCOUNT(0)++;
const double R0 = P(1, 0) - P(0, 0);
const double R1 = P(1, 1) - P(0, 1);
const double R2 = P(1, 2) - P(0, 2);
//printf("Positions P(0) = %f, P(1) = %f |", P(0, 1), P(1, 1));
const double r2 = R0*R0 + R1*R1 + R2*R2;
if (r2 < rc2){
COUNT(0)++;
const double r_m2 = sigma2/r2;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
u(0)+= CV*((r_m6-1.0)*r_m6 + internalshift);
const double r_m8 = r_m4*r_m4;
const double f_tmp = CF*(r_m6 - 0.5)*r_m8;
A(0, 0)+=f_tmp*R0;
A(0, 1)+=f_tmp*R1;
A(0, 2)+=f_tmp*R2;
A(1, 0)-=f_tmp*R0;
A(1, 1)-=f_tmp*R1;
A(1, 2)-=f_tmp*R2;
}
'''
constants = (kernel.Constant('sigma2', self._sigma**2),
kernel.Constant('rc2', self._rc**2),
kernel.Constant('internalshift', self._shift_internal),
kernel.Constant('CF', self._C_F),
kernel.Constant('CV', self._C_V))
reductions = (kernel.Reduction('u', 'u[0]', '+'), )
return kernel.Kernel('LJ_accel_U', kernel_code, constants,
[kernel.Header('stdio.h')], reductions)
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
const double R0 = P(1, 0) - P(0, 0);
const double R1 = P(1, 1) - P(0, 1);
const double R2 = P(1, 2) - P(0, 2);
const double r2 = R0*R0 + R1*R1 + R2*R2;
const double r_m2 = sigma2/r2;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
u(0)+=(r2 < rc2) ? CV*((r_m6-1.0)*r_m6 + internalshift) : 0.0 ;
const double r_m8 = r_m4*r_m4;
const double f_tmp = CF*(r_m6 - 0.5)*r_m8;
A(0, 0)+=(r2 < rc2) ? f_tmp*R0 : 0.0;
A(0, 1)+=(r2 < rc2) ? f_tmp*R1 : 0.0;
A(0, 2)+=(r2 < rc2) ? f_tmp*R2 : 0.0;
A(1, 0)-=(r2 < rc2) ? f_tmp*R0 : 0.0;
A(1, 1)-=(r2 < rc2) ? f_tmp*R1 : 0.0;
A(1, 2)-=(r2 < rc2) ? f_tmp*R2 : 0.0;
'''
constants = (kernel.Constant('sigma2', self._sigma**2),
kernel.Constant('rc2', self._rc**2),
kernel.Constant('internalshift', self._shift_internal),
kernel.Constant('CF', self._C_F),
kernel.Constant('CV', self._C_V))
reductions = (kernel.Reduction('u', 'u[0]', '+'), )
return kernel.Kernel('LJ_accel_U', kernel_code, constants, ['stdio.h'],
reductions)
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
const double R0 = P[1][0] - P[0][0];
const double R1 = P[1][1] - P[0][1];
const double R2 = P[1][2] - P[0][2];
const double r2 = R0*R0 + R1*R1 + R2*R2;
double xn = 0.01;
for(int ix = 0; ix < 2; ix++){
xn = xn*(2.0 - r2*xn);
}
const double r_m2 = sigma2*xn;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
const double _ex = r_m6;
double _et = 1.0, _ep = 1.0, _ef = 1.0, _epx = 1.0;
/*
#pragma novector
for(int _etx = 1; _etx < 21; _etx++){
_epx *= _ex;
_ef *= _ep;
_ep++;
xn = 0.01;
#pragma novector
for(int ix = 0; ix < 10; ix++){
xn = xn*(2.0 - _ef*xn);
}
_et += _epx*xn;
}
*/
u[0]+=CV*((r_m6-1.0)*r_m6 + internalshift);
const double r_m8 = r_m4*r_m4;
const double f_tmp = CF*(r_m6 - 0.5)*r_m8;
A[0][0]+=f_tmp*R0;
A[0][1]+=f_tmp*R1;
A[0][2]+=f_tmp*R2;
A[1][0]-=f_tmp*R0;
A[1][1]-=f_tmp*R1;
A[1][2]-=f_tmp*R2;
'''
constants = (kernel.Constant('sigma2', self._sigma**2),
kernel.Constant('rc2', self._rc**2),
kernel.Constant('internalshift', self._shift_internal),
kernel.Constant('CF', self._C_F),
kernel.Constant('CV', self._C_V))
reductions = (kernel.Reduction('u', 'u[0]', '+'), )
return kernel.Kernel('LJ_accel_U', kernel_code, constants,
[kernel.Header('stdio.h')], reductions)
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
const double R0 = P(1, 0) - P(0, 0);
const double R1 = P(1, 1) - P(0, 1);
const double R2 = P(1, 2) - P(0, 2);
const double r2 = R0*R0 + R1*R1 + R2*R2;
double xn = 0.01;
for(int ix = 0; ix < 10; ix++){
xn = xn*(2.0 - r2*xn);
}
const double r_m2 = sigma2*xn;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
const double _ex = r_m6;
double _et = 1.0, _ep = 1.0, _ef = 1.0, _epx = 1.0;
for(int _etx = 1; _etx < 21; _etx++){
_epx *= _ex;
_ef *= _ep;
_ep++;
xn = 0.01;
for(int ix = 0; ix < 10; ix++){
xn = xn*(2.0 - _ef*xn);
}
_et += _epx*xn;
}
u(0)+=CV*((r_m6-1.0)*r_m6 + internalshift) + _et;
const double r_m8 = r_m4*r_m4;
const double f_tmp = CF*(r_m6 - 0.5)*r_m8;
A(0, 0)+=f_tmp*R0;
A(0, 1)+=f_tmp*R1;
A(0, 2)+=f_tmp*R2;
A(1, 0)-=f_tmp*R0;
A(1, 1)-=f_tmp*R1;
A(1, 2)-=f_tmp*R2;
'''
constants = (kernel.Constant('sigma2', self._sigma**2),
kernel.Constant('rc2', self._rc**2),
kernel.Constant('internalshift', self._shift_internal),
kernel.Constant('CF', self._C_F),
kernel.Constant('CV', self._C_V))
reductions = (kernel.Reduction('u', 'u[0]', '+'), )
return kernel.Kernel('LJ_accel_U', kernel_code, constants, ['stdio.h'],
reductions)