def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
const double R0 = P.j[0] - P.i[0];
const double R1 = P.j[1] - P.i[1];
const double R2 = P.j[2] - P.i[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 f_tmp = CF*(r_m4*r_m2 - 0.5)*r_m4*r_m4;
A.i[0]+= (r2 < rc2) ? f_tmp*R0 : 0.0;
A.i[1]+= (r2 < rc2) ? f_tmp*R1 : 0.0;
A.i[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))
return kernel.Kernel('LJ_accel', kernel_code, constants,
[kernel.Header('stdio.h')])
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) ? 0.5*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;
'''
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))
return kernel.Kernel('LJ_accel_U', kernel_code, constants,
[kernel.Header('stdio.h')])
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 R[3] = {P[1][0] - P[0][0], P[1][1] - P[0][1], P[1][2] - P[0][2]};
double r2 = R[0]*R[0] + R[1]*R[1] + R[2]*R[2];
if (r2 < rc2){
r2=1./r2;
A[0][0]+=r2;
A[0][1]+=r2;
A[0][2]+=r2;
A[1][0]+=r2;
A[1][1]+=r2;
A[1][2]+=r2;
}
'''
constants = (kernel.Constant('rc2', self._rc**2), )
return kernel.Kernel('TestPotential1', kernel_code, constants,
['stdio.h'], None)
def integrate(self, dt=None, t=None):
"""
Integrate state forward in time.
:arg double dt: Time step size.
:arg double t: End time.
"""
print("starting integration")
if dt is not None:
self._dt = dt
if t is not None:
self._T = t
self._max_it = int(math.ceil(self._T / self._dt))
self._constants = [
kernel.Constant('dt', self._dt),
kernel.Constant('dht', 0.5 * self._dt),
]
self._kernel1 = kernel.Kernel('vv1', self._kernel1_code,
self._constants)
self._p1 = loop.ParticleLoop(
self._kernel1, {
'P': self._P(access.W),
'V': self._V(access.W),
'A': self._A(access.R),
'M': self._M(access.R)
})
self._kernel2 = kernel.Kernel('vv2', self._kernel2_code,
self._constants)
self._p2 = loop.ParticleLoop(self._kernel2, {
'V': self._V(access.W),
'A': self._A(access.R),
'M': self._M(access.R)
})
self._update_controller.execute_boundary_conditions()
self._sim.forces_update()
self.timer.start()
self._velocity_verlet_integration()
self.timer.pause()
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;
if (r2 < rc2) {
const double r = sqrt(r2);
// \\exp{-B*r}
const double exp_mbr = exp(_MB*r);
// r^{-2, -4, -6}
const double r_m1 = 1.0/r;
const double r_m2 = r_m1*r_m1;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
// \\frac{C}{r^6}
const double crm6 = _C*r_m6;
// A \\exp{-Br} - \\frac{C}{r^6}
u(0)+= _A*exp_mbr - crm6 + internalshift;
// AB \\exp{-Br} - \\frac{C}{r^6}*\\frac{6}{r}
const double term2 = crm6*(-6.0)*r_m1;
const double f_tmp = _AB * exp_mbr + term2;
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('_A',
self.a), kernel.Constant('_AB', self.ab),
kernel.Constant('_B',
self.b), kernel.Constant('_MB', self.mb),
kernel.Constant('_C', self.c),
kernel.Constant('rc2', self.rc**2),
kernel.Constant('internalshift', self._shift_internal))
return kernel.Kernel(
'BuckinghamV', kernel_code, constants,
[kernel.Header('stdio.h'),
kernel.Header('math.h')])
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
//N_f = 27
const double R0 = P.j[0] - P.i[0];
const double R1 = P.j[1] - P.i[1];
const double R2 = P.j[2] - P.i[2];
const double r2 = R0*R0 + R1*R1 + R2*R2;
if (r2 < rc2){
const double r_m2 = sigma2/r2;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
u[0] += 0.5*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.i[0] += f_tmp*R0;
A.i[1] += f_tmp*R1;
A.i[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))
return kernel.Kernel('LJ_accel_U', kernel_code, constants,
[kernel.Header('stdio.h')])
def _build_libs(self, dt):
kernel1_code = '''
const double M_tmp = 1.0/M(0);
V(0) += dht*F(0)*M_tmp;
V(1) += dht*F(1)*M_tmp;
V(2) += dht*F(2)*M_tmp;
P(0) += dt*V(0);
P(1) += dt*V(1);
P(2) += dt*V(2);
'''
kernel2_code = '''
const double M_tmp = 1.0/M(0);
V(0) += dht*F(0)*M_tmp;
V(1) += dht*F(1)*M_tmp;
V(2) += dht*F(2)*M_tmp;
'''
constants = [
kernel.Constant('dt', dt),
kernel.Constant('dht', 0.5 * dt),
]
kernel1 = kernel.Kernel('vv1', kernel1_code, constants)
self._p1 = self._looping_method(kernel=kernel1,
dat_dict={
'P': self._p(access.W),
'V': self._v(access.W),
'F': self._f(access.R),
'M': self._m(access.R)
})
kernel2 = kernel.Kernel('vv2', kernel2_code, constants)
self._p2 = self._looping_method(kernel=kernel2,
dat_dict={
'V': self._v(access.W),
'F': self._f(access.R),
'M': self._m(access.R)
})
def kernel(self):
"""
Returns a kernel class for the potential.
"""
kernel_code = '''
const double R0 = P.j[0] - P.i[0];
const double R1 = P.j[1] - P.i[1];
const double R2 = P.j[2] - P.i[2];
const double r2 = R0*R0 + R1*R1 + R2*R2;
const double r = sqrt(r2);
// \\exp{-B*r}
const double exp_mbr = exp(_MB*r);
// r^{-2, -4, -6}
const double r_m1 = 1.0/r;
const double r_m2 = r_m1*r_m1;
const double r_m4 = r_m2*r_m2;
const double r_m6 = r_m4*r_m2;
// \\frac{C}{r^6}
const double crm6 = _C*r_m6;
// A \\exp{-Br} - \\frac{C}{r^6}
u[0]+= (r2 < rc2) ? 0.5*(_A*exp_mbr - crm6 + internalshift) : 0.0;
// = AB \\exp{-Br} - \\frac{C}{r^6}*\\frac{6}{r}
const double term2 = crm6*(-6.0)*r_m1;
const double f_tmp = _AB * exp_mbr + term2;
A.i[0]+= (r2 < rc2) ? f_tmp*R0 : 0.0;
A.i[1]+= (r2 < rc2) ? f_tmp*R1 : 0.0;
A.i[2]+= (r2 < rc2) ? f_tmp*R2 : 0.0;
'''
constants = (kernel.Constant('_A',
self.a), kernel.Constant('_AB', self.ab),
kernel.Constant('_B',
self.b), kernel.Constant('_MB', self.mb),
kernel.Constant('_C', self.c),
kernel.Constant('rc2', self.rc**2),
kernel.Constant('internalshift', self._shift_internal))
return kernel.Kernel(
'BuckinghamV', kernel_code, constants,
[kernel.Header('stdio.h'),
kernel.Header('math.h')])
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)
def __init__(self, state, rmax=None, rsteps=100):
self._count = 0
self._state = state
self._extent = self._state.domain.extent
self._P = self._state.positions
self._N = self._state.npart_local
self._rmax = rmax
if self._rmax is None:
self._rmax = 0.5 * np.min(self._extent.data)
self._rsteps = rsteps
self._gr = data.ScalarArray(ncomp=self._rsteps, dtype=ctypes.c_int)
self._gr.scale(0.0)
_headers = ['math.h', 'stdio.h']
_kernel = '''
double R0 = P(1, 0) - P(0, 0);
double R1 = P(1, 1) - P(0, 1);
double R2 = P(1, 2) - P(0, 2);
if (abs_md(R0) > exto20 ) { R0 += isign(R0) * extent0 ; }
if (abs_md(R1) > exto21 ) { R1 += isign(R1) * extent1 ; }
if (abs_md(R2) > exto22 ) { R2 += isign(R2) * extent2 ; }
const double r2 = R0*R0 + R1*R1 + R2*R2;
if (r2 < rmax2){
double r20=0.0, r21 = r2;
r21 = sqrt(r2);
#pragma omp atomic
GR[(int) (abs_md(r21* rstepsoverrmax))]++;
}
'''
_constants = (kernel.Constant('rmaxoverrsteps',
0.2 * self._rmax / self._rsteps),
kernel.Constant('rstepsoverrmax',
self._rsteps / self._rmax),
kernel.Constant('rmax2', self._rmax**2),
kernel.Constant('extent0', self._extent[0]),
kernel.Constant('extent1', self._extent[1]),
kernel.Constant('extent2', self._extent[2]),
kernel.Constant('exto20', 0.5 * self._extent[0]),
kernel.Constant('exto21', 0.5 * self._extent[1]),
kernel.Constant('exto22', 0.5 * self._extent[2]))
_grkernel = kernel.Kernel('radial_distro_periodic_static',
_kernel,
_constants,
headers=_headers)
_datdict = {'P': self._P, 'GR': self._gr}
self._p = pairloop.DoubleAllParticleLoop(self._N,
kernel=_grkernel,
dat_dict=_datdict)
self.timer = ppmd.opt.Timer(runtime.TIMER, 0)
def integrate_thermostat(self, dt=None, t=None, temp=273.15, nu=1.0):
"""
Integrate state forward in time.
:arg double dt: Time step size.
:arg double t: End time.
:arg double temp: Temperature of heat bath.
"""
self._Temp = temp
self._nu = nu
if dt is not None:
self._dt = dt
if t is not None:
self._T = t
self._max_it = int(math.ceil(self._T / self._dt))
self._constants1 = [
kernel.Constant('dt', self._dt),
kernel.Constant('dht', 0.5 * self._dt),
]
self._kernel1 = kernel.Kernel('vv1', self._kernel1_code,
self._constants1)
self._p1 = loop.ParticleLoop(self._kernel1, {
'P': self._P,
'V': self._V,
'A': self._A,
'M': self._M
})
self._kernel2_thermostat_code = '''
//Anderson thermostat here.
//probably horrific random code.
const double tmp_rand_max = 1.0/RAND_MAX;
if (rand()*tmp_rand_max < rate) {
//Box-Muller method.
const double scale = sqrt(temperature/M(0));
const double stmp = scale*sqrt(-2.0*log(rand()*tmp_rand_max));
const double V0 = 2.0*M_PI*rand()*tmp_rand_max;
V(0) = stmp*cos(V0);
V(1) = stmp*sin(V0);
V(2) = scale*sqrt(-2.0*log(rand()*tmp_rand_max))*cos(2.0*M_PI*rand()*tmp_rand_max);
}
else {
const double M_tmp = 1./M(0);
V(0) += dht*A(0)*M_tmp;
V(1) += dht*A(1)*M_tmp;
V(2) += dht*A(2)*M_tmp;
}
'''
self._constants2_thermostat = [
kernel.Constant('rate', self._dt * self._nu),
kernel.Constant('dt', self._dt),
kernel.Constant('dht', 0.5 * self._dt),
kernel.Constant('temperature', self._Temp),
]
self._kernel2_thermostat = kernel.Kernel(
'vv2_thermostat',
self._kernel2_thermostat_code,
self._constants2_thermostat,
headers=['math.h', 'stdlib.h', 'time.h', 'stdio.h'])
self._p2_thermostat = loop.ParticleLoop(self._kernel2_thermostat, {
'V': self._V,
'A': self._A,
'M': self._M
})
_t = ppmd.opt.Timer(runtime.TIMER, 0, start=True)
self._velocity_verlet_integration_thermostat()
_t.stop("VelocityVerletAnderson")