def calculateEsurf(surf_array, field_array, param, kernel):
REAL = param.REAL
par_reac = parameters()
par_reac = param
par_reac.threshold = 0.05
par_reac.P = 7
par_reac.theta = 0.0
par_reac.Nm = (par_reac.P + 1) * (par_reac.P + 2) * (par_reac.P + 3) / 6
ind_reac = index_constant()
computeIndices(par_reac.P, ind_reac)
precomputeTerms(par_reac.P, ind_reac)
par_reac.Nk = 13 # Number of Gauss points per side for semi-analytical integrals
cal2J = 4.184
C0 = param.qe**2 * param.Na * 1e-3 * 1e10 / (cal2J * param.E_0)
E_surf = []
ff = -1
for f in param.E_field:
parent_surf = surf_array[field_array[f].parent[0]]
if parent_surf.surf_type == 'dirichlet_surface':
ff += 1
print 'Calculating surface energy around region %i, stored in E_surf[%i]' % (
f, ff)
Esurf_aux = -numpy.sum(-parent_surf.Eout * parent_surf.dphi *
parent_surf.phi * parent_surf.Area)
E_surf.append(0.5 * C0 * Esurf_aux)
elif parent_surf.surf_type == 'neumann_surface':
ff += 1
print 'Calculating surface energy around region %i, stored in E_surf[%i]' % (
f, ff)
Esurf_aux = numpy.sum(-parent_surf.Eout * parent_surf.dphi *
parent_surf.phi * parent_surf.Area)
E_surf.append(0.5 * C0 * Esurf_aux)
return E_surf
def calculateEsurf(surf_array, field_array, param, kernel):
REAL = param.REAL
par_reac = parameters()
par_reac = param
par_reac.threshold = 0.05
par_reac.P = 7
par_reac.theta = 0.0
par_reac.Nm= (par_reac.P+1)*(par_reac.P+2)*(par_reac.P+3)/6
ind_reac = index_constant()
computeIndices(par_reac.P, ind_reac)
precomputeTerms(par_reac.P, ind_reac)
par_reac.Nk = 13 # Number of Gauss points per side for semi-analytical integrals
cal2J = 4.184
C0 = param.qe**2*param.Na*1e-3*1e10/(cal2J*param.E_0)
E_surf = []
ff = -1
for f in param.E_field:
parent_surf = surf_array[field_array[f].parent[0]]
if parent_surf.surf_type == 'dirichlet_surface':
ff += 1
print 'Calculating surface energy around region %i, stored in E_surf[%i]'%(f,ff)
Esurf_aux = -sum(-parent_surf.Eout*parent_surf.dphi*parent_surf.phi*parent_surf.Area)
E_surf.append(0.5*C0*Esurf_aux)
elif parent_surf.surf_type == 'neumann_surface':
ff += 1
print 'Calculating surface energy around region %i, stored in E_surf[%i]'%(f,ff)
Esurf_aux = sum(-parent_surf.Eout*parent_surf.dphi*parent_surf.phi*parent_surf.Area)
E_surf.append(0.5*C0*Esurf_aux)
return E_surf
# import modules for testing
#from mpl_toolkits.mplot3d import Axes3D
#import matplotlib.pyplot as plt
### Time stamp
timestamp = time.localtime()
print 'Run started on:'
print '\tDate: %i/%i/%i' % (timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday)
print '\tTime: %i:%i:%i' % (timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec)
TIC = time.time()
### Read parameters
param = parameters()
precision = readParameters(param, sys.argv[1])
configFile = sys.argv[2]
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) / 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(
param.NCRIT / float(param.BSZ))) # CUDA blocks that fit per twig
### Generate array of fields
field_array = initializeField(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initializeSurf(field_array, configFile, param)
### Fill surface class
from FMMutils import * from cuda_kernels import kernels # import modules for testing #from mpl_toolkits.mplot3d import Axes3D #import matplotlib.pyplot as plt ### Time stamp timestamp = time.localtime() print 'Run started on:' print '\tDate: %i/%i/%i'%(timestamp.tm_year,timestamp.tm_mon,timestamp.tm_mday) print '\tTime: %i:%i:%i'%(timestamp.tm_hour,timestamp.tm_min,timestamp.tm_sec) TIC = time.time() ### Read parameters param = parameters() precision = readParameters(param,sys.argv[1]) configFile = sys.argv[2] param.Nm = (param.P+1)*(param.P+2)*(param.P+3)/6 # Number of terms in Taylor expansion param.BlocksPerTwig = int(numpy.ceil(param.NCRIT/float(param.BSZ))) # CUDA blocks that fit per twig ### Generate array of fields field_array = initializeField(configFile, param) ### Generate array of surfaces and read in elements surf_array = initializeSurf(field_array, configFile, param) ### Fill surface class time_sort = 0. for i in range(len(surf_array)):
def calculateEsolv(surf_array, field_array, param, kernel):
REAL = param.REAL
par_reac = parameters()
par_reac = param
par_reac.threshold = 0.05
par_reac.P = 7
par_reac.theta = 0.0
par_reac.Nm = (par_reac.P + 1) * (par_reac.P + 2) * (par_reac.P + 3) / 6
ind_reac = index_constant()
computeIndices(par_reac.P, ind_reac)
precomputeTerms(par_reac.P, ind_reac)
par_reac.Nk = 13 # Number of Gauss points per side for semi-analytical integrals
cal2J = 4.184
C0 = param.qe**2 * param.Na * 1e-3 * 1e10 / (cal2J * param.E_0)
E_solv = []
ff = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type != 'dirichlet_surface' and parent_type != 'neumann_surface':
E_solv_aux = 0
ff += 1
print 'Calculating solvation energy for region %i, stored in E_solv[%i]' % (
f, ff)
AI_int = 0
Naux = 0
phi_reac = numpy.zeros(len(field_array[f].q))
# First look at CHILD surfaces
# Need to account for normals pointing outwards
# and E_hat coefficient (as region is outside and
# dphi_dn is defined inside)
for i in field_array[f].child:
s = surf_array[i]
s.xk, s.wk = GQ_1D(par_reac.Nk)
s.xk = REAL(s.xk)
s.wk = REAL(s.wk)
for C in range(len(s.tree)):
s.tree[C].M = numpy.zeros(par_reac.Nm)
s.tree[C].Md = numpy.zeros(par_reac.Nm)
Naux += len(s.triangle)
# Coefficient to account for dphi_dn defined in
# interior but calculation done in exterior
C1 = s.E_hat
if param.GPU == 0:
phi_aux, AI = get_phir(s.phi, C1 * s.dphi, s,
field_array[f].xq, s.tree, par_reac,
ind_reac)
elif param.GPU == 1:
phi_aux, AI = get_phir_gpu(s.phi, C1 * s.dphi, s,
field_array[f], par_reac,
kernel)
AI_int += AI
phi_reac -= phi_aux # Minus sign to account for normal pointing out
# Now look at PARENT surface
if len(field_array[f].parent) > 0:
i = field_array[f].parent[0]
s = surf_array[i]
s.xk, s.wk = GQ_1D(par_reac.Nk)
s.xk = REAL(s.xk)
s.wk = REAL(s.wk)
for C in range(len(s.tree)):
s.tree[C].M = numpy.zeros(par_reac.Nm)
s.tree[C].Md = numpy.zeros(par_reac.Nm)
Naux += len(s.triangle)
if param.GPU == 0:
phi_aux, AI = get_phir(s.phi, s.dphi, s, field_array[f].xq,
s.tree, par_reac, ind_reac)
elif param.GPU == 1:
phi_aux, AI = get_phir_gpu(s.phi, s.dphi, s,
field_array[f], par_reac,
kernel)
AI_int += AI
phi_reac += phi_aux
E_solv_aux += 0.5 * C0 * numpy.sum(field_array[f].q * phi_reac)
E_solv.append(E_solv_aux)
print '%i of %i analytical integrals for phi_reac calculation in region %i' % (
AI_int / len(field_array[f].xq), Naux, f)
return E_solv
def load_params(self,opts):
return parameters(parfile=opts.param_filename)
def calculateEsolv(surf_array, field_array, param, kernel):
REAL = param.REAL
par_reac = parameters()
par_reac = param
par_reac.threshold = 0.05
par_reac.P = 7
par_reac.theta = 0.0
par_reac.Nm= (par_reac.P+1)*(par_reac.P+2)*(par_reac.P+3)/6
ind_reac = index_constant()
computeIndices(par_reac.P, ind_reac)
precomputeTerms(par_reac.P, ind_reac)
par_reac.Nk = 13 # Number of Gauss points per side for semi-analytical integrals
cal2J = 4.184
C0 = param.qe**2*param.Na*1e-3*1e10/(cal2J*param.E_0)
E_solv = []
ff = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type != 'dirichlet_surface' and parent_type != 'neumann_surface':
E_solv_aux = 0
ff += 1
print 'Calculating solvation energy for region %i, stored in E_solv[%i]'%(f,ff)
AI_int = 0
Naux = 0
phi_reac = zeros(len(field_array[f].q))
# First look at CHILD surfaces
# Need to account for normals pointing outwards
# and E_hat coefficient (as region is outside and
# dphi_dn is defined inside)
for i in field_array[f].child:
s = surf_array[i]
s.xk,s.wk = GQ_1D(par_reac.Nk)
s.xk = REAL(s.xk)
s.wk = REAL(s.wk)
for C in range(len(s.tree)):
s.tree[C].M = zeros(par_reac.Nm)
s.tree[C].Md = zeros(par_reac.Nm)
Naux += len(s.triangle)
# Coefficient to account for dphi_dn defined in
# interior but calculation done in exterior
C1 = s.E_hat
if param.GPU==0:
phi_aux, AI = get_phir(s.phi, C1*s.dphi, s, field_array[f].xq, s.tree, par_reac, ind_reac)
elif param.GPU==1:
phi_aux, AI = get_phir_gpu(s.phi, C1*s.dphi, s, field_array[f], par_reac, kernel)
AI_int += AI
phi_reac -= phi_aux # Minus sign to account for normal pointing out
# Now look at PARENT surface
if len(field_array[f].parent)>0:
i = field_array[f].parent[0]
s = surf_array[i]
s.xk,s.wk = GQ_1D(par_reac.Nk)
s.xk = REAL(s.xk)
s.wk = REAL(s.wk)
for C in range(len(s.tree)):
s.tree[C].M = zeros(par_reac.Nm)
s.tree[C].Md = zeros(par_reac.Nm)
Naux += len(s.triangle)
if param.GPU==0:
phi_aux, AI = get_phir(s.phi, s.dphi, s, field_array[f].xq, s.tree, par_reac, ind_reac)
elif param.GPU==1:
phi_aux, AI = get_phir_gpu(s.phi, s.dphi, s, field_array[f], par_reac, kernel)
AI_int += AI
phi_reac += phi_aux
E_solv_aux += 0.5*C0*sum(field_array[f].q*phi_reac)
E_solv.append(E_solv_aux)
print '%i of %i analytical integrals for phi_reac calculation in region %i'%(AI_int/len(field_array[f].xq),Naux, f)
return E_solv
