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 _init_self_interaction_lib(self):
if self.shared_memory in ('thread', 'omp'):
PL = loop.ParticleLoopOMP
else:
PL = loop.ParticleLoop
with open(str(_SRC_DIR) + '/EwaldOrthSource/SelfInteraction.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = (kernel.Header(block=_cont_header_src %
self._subvars), )
with open(str(_SRC_DIR) + '/EwaldOrthSource/SelfInteraction.cpp',
'r') as fh:
_cont_source = fh.read()
_real_kernel = kernel.Kernel(name='self_interaction_part',
code=_cont_source,
headers=_cont_header)
self._self_interaction_lib = PL(
kernel=_real_kernel,
dat_dict={
'Q': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.READ),
'u': self._vars['self_interaction_energy'](access.INC_ZERO)
})
with open(
str(_SRC_DIR) + '/EwaldOrthSource/SelfInteractionPot.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = (kernel.Header(block=_cont_header_src %
self._subvars), )
with open(
str(_SRC_DIR) + '/EwaldOrthSource/SelfInteractionPot.cpp',
'r') as fh:
_cont_source = fh.read()
_real_kernel = kernel.Kernel(name='self_interaction_part_pot',
code=_cont_source,
headers=_cont_header)
self._self_interaction_pot_lib = PL(
kernel=_real_kernel,
dat_dict={
'Q': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.READ),
'UPP': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.INC),
'u': self._vars['self_interaction_energy'](access.INC_ZERO)
})
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;
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 = '''
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 = '''
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 _init_near_potential_lib(self):
# real space energy and force kernel
with open(
str(_SRC_DIR) +
'/EwaldOrthSource/EvaluateNearPotentialField.h', 'r') as fh:
_cont_header_src = fh.read()
_cont_header = (kernel.Header(block=_cont_header_src %
self._subvars), )
with open(
str(_SRC_DIR) +
'/EwaldOrthSource/EvaluateNearPotentialField.cpp', 'r') as fh:
_cont_source = fh.read()
_real_kernel = kernel.Kernel(name='real_space_part',
code=_cont_source,
headers=_cont_header)
if self.shell_width is None:
rn = self.real_cutoff * 1.05
else:
rn = self.real_cutoff + self.shell_width
PPL = pairloop.CellByCellOMP
self._near_potential_field = PPL(
kernel=_real_kernel,
dat_dict={
'P': data.ParticleDat(ncomp=3,
dtype=ctypes.c_double)(access.READ),
'Q': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.READ),
'M': data.ParticleDat(ncomp=1,
dtype=ctypes.c_int)(access.READ),
'u': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.INC),
},
shell_cutoff=rn)
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 _init_real_space_lib(self):
# real space energy and force kernel
with open(
str(_SRC_DIR) + '/EwaldOrthSource/RealSpaceForceEnergy.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = (kernel.Header(block=_cont_header_src %
self._subvars), )
with open(
str(_SRC_DIR) + '/EwaldOrthSource/RealSpaceForceEnergy.cpp',
'r') as fh:
_cont_source = fh.read()
_real_kernel = kernel.Kernel(name='real_space_part',
code=_cont_source,
headers=_cont_header)
if self.shell_width is None:
rn = self.real_cutoff * 1.05
else:
rn = self.real_cutoff + self.shell_width
if self.shared_memory in ('thread', 'omp'):
PPL = pairloop.PairLoopNeighbourListNSOMP
else:
PPL = pairloop.PairLoopNeighbourListNS
self._real_space_pairloop = PPL(
kernel=_real_kernel,
dat_dict={
'P': data.ParticleDat(ncomp=3,
dtype=ctypes.c_double)(access.READ),
'Q': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.READ),
'F': data.ParticleDat(ncomp=3,
dtype=ctypes.c_double)(access.INC),
'u': self._vars['real_space_energy'](access.INC_ZERO)
},
shell_cutoff=rn)
# real space energy and force kernel and per particle potential
with open(
str(_SRC_DIR) + '/EwaldOrthSource/RealSpaceForceEnergyPot.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = (kernel.Header(block=_cont_header_src %
self._subvars), )
with open(
str(_SRC_DIR) + '/EwaldOrthSource/RealSpaceForceEnergyPot.cpp',
'r') as fh:
_cont_source = fh.read()
_real_kernel = kernel.Kernel(name='real_space_part_pot',
code=_cont_source,
headers=_cont_header)
self._real_space_pairloop_pot = PPL(
kernel=_real_kernel,
dat_dict={
'P': data.ParticleDat(ncomp=3,
dtype=ctypes.c_double)(access.READ),
'Q': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.READ),
'UPP': data.ParticleDat(ncomp=1,
dtype=ctypes.c_double)(access.INC),
'F': data.ParticleDat(ncomp=3,
dtype=ctypes.c_double)(access.INC),
'u': self._vars['real_space_energy'](access.INC_ZERO)
},
shell_cutoff=rn)
def _init_libs(self):
# reciprocal contribution calculation
with open(str(_SRC_DIR) + '/EwaldOrthSource/AccumulateRecip.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = kernel.Header(block=_cont_header_src % self._subvars)
with open(str(_SRC_DIR) + '/EwaldOrthSource/AccumulateRecip.cpp',
'r') as fh:
_cont_source = fh.read()
_cont_kernel = kernel.Kernel(name='reciprocal_contributions',
code=_cont_source,
headers=_cont_header)
if self.shared_memory in ('thread', 'omp'):
PL = loop.ParticleLoopOMP
else:
PL = loop.ParticleLoop
self._cont_lib = PL(
kernel=_cont_kernel,
dat_dict={
'Positions':
data.ParticleDat(ncomp=3, dtype=ctypes.c_double)(access.READ),
'Charges':
data.ParticleDat(ncomp=1, dtype=ctypes.c_double)(access.READ),
'RecipSpace':
self._vars['recip_space_kernel'](access.INC_ZERO)
})
# reciprocal extract forces plus energy
with open(
str(_SRC_DIR) + '/EwaldOrthSource/ExtractForceEnergy.h',
'r') as fh:
_cont_header_src = fh.read()
_cont_header = kernel.Header(block=_cont_header_src % self._subvars)
with open(
str(_SRC_DIR) + '/EwaldOrthSource/ExtractForceEnergy.cpp',
'r') as fh:
_cont_source = fh.read()
_cont_kernel = kernel.Kernel(name='reciprocal_force_energy',
code=_cont_source,
headers=_cont_header)
self._extract_force_energy_lib = PL(
kernel=_cont_kernel,
dat_dict={
'Positions':
data.ParticleDat(ncomp=3, dtype=ctypes.c_double)(access.READ),
'Forces':
data.ParticleDat(ncomp=3, dtype=ctypes.c_double)(access.INC),
'Energy':
self._vars['recip_space_energy'](access.INC_ZERO),
'Charges':
data.ParticleDat(ncomp=1, dtype=ctypes.c_double)(access.READ),
'RecipSpace':
self._vars['recip_space_kernel'](access.READ),
'CoeffSpace':
self._vars['coeff_space_kernel'](access.READ)
})
self._extract_force_energy_pot_lib = None
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)