Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
A
add_child() (in module pygbe.tree.FMMutils)
addSources() (in module pygbe.tree.FMMutils)
addSources2() (in module pygbe.tree.FMMutils)
addSources3() (in module pygbe.tree.FMMutils)
AI_int (pygbe.classes.Timing attribute)
an_P() (in module pygbe.util.an_solution)
an_spherical() (in module pygbe.util.an_solution)
apply_givens() (in module pygbe.gmres)
area (pygbe.classes.Surface attribute)
areaDev (pygbe.classes.Surface attribute)
areaSort (pygbe.classes.Surface attribute)
B
BlocksPerTwig (pygbe.classes.Parameters attribute)
BSZ (pygbe.classes.Parameters attribute)
C
calc_aux() (in module pygbe.matrixfree)
calc_centers() (pygbe.classes.Surface method)
calc_distance() (pygbe.classes.Surface method)
calc_norms() (pygbe.classes.Surface method)
calculate_solvation_energy() (in module pygbe.matrixfree)
calculate_surface_energy() (in module pygbe.matrixfree)
Cell (class in pygbe.tree.FMMutils)
check_file_exists() (in module pygbe.main)
check_for_nvcc() (in module pygbe.main)
child (pygbe.classes.Field attribute)
(pygbe.tree.FMMutils.Cell attribute)
combII (pygbe.classes.IndexConstant attribute)
combJJ (pygbe.classes.IndexConstant attribute)
combKK (pygbe.classes.IndexConstant attribute)
computeIndices() (in module pygbe.tree.FMMutils)
constant_charge_single_energy() (in module pygbe.util.an_solution)
constant_charge_single_point() (in module pygbe.util.an_solution)
constant_charge_single_potential() (in module pygbe.util.an_solution)
constant_charge_twosphere_dissimilar() (in module pygbe.util.an_solution)
constant_charge_twosphere_identical() (in module pygbe.util.an_solution)
constant_potential_single_charge() (in module pygbe.util.an_solution)
constant_potential_single_energy() (in module pygbe.util.an_solution)
constant_potential_single_point() (in module pygbe.util.an_solution)
constant_potential_twosphere() (in module pygbe.util.an_solution)
constant_potential_twosphere_2() (in module pygbe.util.an_solution)
constant_potential_twosphere_dissimilar() (in module pygbe.util.an_solution)
constant_potential_twosphere_identical() (in module pygbe.util.an_solution)
coulomb (pygbe.classes.Field attribute)
coulomb_energy() (in module pygbe.matrixfree)
D
dataTransfer() (in module pygbe.gpuio)
define_regions() (pygbe.classes.Surface method)
define_surface() (pygbe.classes.Surface method)
dphi (pygbe.classes.Surface attribute)
E
E (pygbe.classes.Field attribute)
E_0 (pygbe.classes.Parameters attribute)
E_field (pygbe.classes.Parameters attribute)
E_hat (pygbe.classes.Surface attribute)
Ein (pygbe.classes.Surface attribute)
Eout (pygbe.classes.Surface attribute)
eps (pygbe.classes.Parameters attribute)
Event (class in pygbe.classes)
F
Field (class in pygbe.classes)
fill_phi() (pygbe.classes.Surface method)
fill_surface() (pygbe.classes.Surface method)
find_config_files() (in module pygbe.main)
findTwigs() (in module pygbe.tree.FMMutils)
flush() (pygbe.main.Logger method)
G
generate_preconditioner() (pygbe.classes.Surface method)
generateList() (in module pygbe.tree.FMMutils)
generateRHS() (in module pygbe.matrixfree)
generateRHS_gpu() (in module pygbe.matrixfree)
generateTree() (in module pygbe.tree.FMMutils)
get_gauss_points() (pygbe.classes.Surface method)
get_K() (in module pygbe.util.an_solution)
get_phir() (in module pygbe.projection)
get_phir_gpu() (in module pygbe.projection)
getMultipole() (in module pygbe.tree.FMMutils)
getWeights() (in module pygbe.quadrature)
gmres_dot() (in module pygbe.matrixfree)
gmres_mgs() (in module pygbe.gmres)
GPU (pygbe.classes.Parameters attribute)
GQ_1D() (in module pygbe.util.semi_analytical)
I
II (pygbe.classes.IndexConstant attribute)
IImii (pygbe.classes.IndexConstant attribute)
index (pygbe.classes.IndexConstant attribute)
index_large (pygbe.classes.IndexConstant attribute)
index_ptr (pygbe.classes.IndexConstant attribute)
index_small (pygbe.classes.IndexConstant attribute)
IndexConstant (class in pygbe.classes)
indexDev (pygbe.classes.IndexConstant attribute)
initialize_field() (in module pygbe.class_initialization)
initialize_surface() (in module pygbe.class_initialization)
interactionList() (in module pygbe.tree.FMMutils)
intSide() (in module pygbe.util.semi_analytical)
J
JJ (pygbe.classes.IndexConstant attribute)
JJmjj (pygbe.classes.IndexConstant attribute)
K
K (pygbe.classes.Parameters attribute)
K_fine (pygbe.classes.Parameters attribute)
kappa (pygbe.classes.Field attribute)
(pygbe.classes.Parameters attribute)
kappa_in (pygbe.classes.Surface attribute)
kappa_out (pygbe.classes.Surface attribute)
kDev (pygbe.classes.Surface attribute)
kernels() (in module pygbe.tree.cuda_kernels)
KK (pygbe.classes.IndexConstant attribute)
KKmkk (pygbe.classes.IndexConstant attribute)
L
lineInt() (in module pygbe.util.semi_analytical)
list_ready (pygbe.tree.FMMutils.Cell attribute)
load_charges() (pygbe.classes.Field method)
locate_s_in_RHS() (in module pygbe.matrixfree)
Logger (class in pygbe.main)
LorY (pygbe.classes.Field attribute)
LorY_in (pygbe.classes.Surface attribute)
LorY_out (pygbe.classes.Surface attribute)
M
M (pygbe.tree.FMMutils.Cell attribute)
M2P_gpu() (in module pygbe.tree.FMMutils)
M2P_list (pygbe.classes.Surface attribute)
(pygbe.tree.FMMutils.Cell attribute)
M2P_lstDev (pygbe.classes.Surface attribute)
M2P_nonvec() (in module pygbe.tree.FMMutils)
M2P_size (pygbe.tree.FMMutils.Cell attribute)
M2P_sort() (in module pygbe.tree.FMMutils)
M2PKt_gpu() (in module pygbe.tree.FMMutils)
M2PKt_sort() (in module pygbe.tree.FMMutils)
main() (in module pygbe.main)
max_iter (pygbe.classes.Parameters attribute)
Md (pygbe.tree.FMMutils.Cell attribute)
molecule_constant_charge() (in module pygbe.util.an_solution)
molecule_constant_potential() (in module pygbe.util.an_solution)
N
N (pygbe.classes.Parameters attribute)
Na (pygbe.classes.Parameters attribute)
nchild (pygbe.tree.FMMutils.Cell attribute)
NCRIT (pygbe.classes.Parameters attribute)
Neq (pygbe.classes.Parameters attribute)
Nk (pygbe.classes.Parameters attribute)
Nm (pygbe.classes.Parameters attribute)
nonselfExterior() (in module pygbe.matrixfree)
nonselfInterior() (in module pygbe.matrixfree)
normal (pygbe.classes.Surface attribute)
Nround (pygbe.classes.Parameters attribute)
nsource (pygbe.tree.FMMutils.Cell attribute)
ntarget (pygbe.tree.FMMutils.Cell attribute)
O
offMltDev (pygbe.classes.Surface attribute)
offsetMlt (pygbe.classes.Surface attribute)
offsetSource (pygbe.classes.Surface attribute)
offsetTarget (pygbe.classes.Surface attribute)
offsetTwigs (pygbe.classes.Surface attribute)
offSrcDev (pygbe.classes.Surface attribute)
offTwgDev (pygbe.classes.Surface attribute)
P
P (pygbe.classes.Parameters attribute)
P2P_gpu() (in module pygbe.tree.FMMutils)
P2P_list (pygbe.classes.Surface attribute)
(pygbe.tree.FMMutils.Cell attribute)
P2P_lstDev (pygbe.classes.Surface attribute)
P2P_nonvec() (in module pygbe.tree.FMMutils)
P2P_sort() (in module pygbe.tree.FMMutils)
P2PKt_gpu() (in module pygbe.tree.FMMutils)
P2PKt_sort() (in module pygbe.tree.FMMutils)
Parameters (class in pygbe.classes)
parent (pygbe.classes.Field attribute)
(pygbe.tree.FMMutils.Cell attribute)
phi (pygbe.classes.Surface attribute)
phi0 (pygbe.classes.Surface attribute)
pot (pygbe.classes.Field attribute)
precomputeTerms() (in module pygbe.tree.FMMutils)
Precond (pygbe.classes.Surface attribute)
print_summary() (in module pygbe.output)
project() (in module pygbe.projection)
project_Kt() (in module pygbe.projection)
pygbe (module)
pygbe.class_initialization (module)
pygbe.classes (module)
pygbe.gmres (module)
pygbe.gpuio (module)
pygbe.main (module)
pygbe.matrixfree (module)
pygbe.output (module)
pygbe.projection (module)
pygbe.quadrature (module)
pygbe.tree (module)
pygbe.tree.calculateMultipoles (module)
pygbe.tree.cuda_kernels (module)
pygbe.tree.direct (module)
pygbe.tree.FMMutils (module)
pygbe.tree.multipole (module)
pygbe.util (module)
pygbe.util.an_solution (module)
pygbe.util.read_data (module)
pygbe.util.semi_analytical (module)
pygbe.util.semi_analyticalwrap (module)
Q
q (pygbe.classes.Field attribute)
q_gpu (pygbe.classes.Field attribute)
qe (pygbe.classes.Parameters attribute)
quadratureRule_fine() (in module pygbe.quadrature)
R
r (pygbe.tree.FMMutils.Cell attribute)
read_fields() (in module pygbe.util.read_data)
read_inputs() (in module pygbe.main)
read_surface() (in module pygbe.util.read_data)
read_triangle() (in module pygbe.util.read_data)
read_vertex() (in module pygbe.util.read_data)
readCheck() (in module pygbe.util.read_data)
readcrd() (in module pygbe.util.read_data)
readElectricField() (in module pygbe.util.read_data)
readParameters() (in module pygbe.util.read_data)
readpqr() (in module pygbe.util.read_data)
REAL (pygbe.classes.Parameters attribute)
record() (pygbe.classes.Event method)
resolve_relative_config_file() (in module pygbe.main)
restart (pygbe.classes.Parameters attribute)
S
SA_arr() (in module pygbe.util.semi_analytical)
selfASC() (in module pygbe.matrixfree)
selfExterior() (in module pygbe.matrixfree)
selfInterior() (in module pygbe.matrixfree)
sglInt_ext (pygbe.classes.Surface attribute)
sglInt_extDev (pygbe.classes.Surface attribute)
sglInt_extSort (pygbe.classes.Surface attribute)
sglInt_int (pygbe.classes.Surface attribute)
sglInt_intDev (pygbe.classes.Surface attribute)
sglInt_intSort (pygbe.classes.Surface attribute)
sizeTarDev (pygbe.classes.Surface attribute)
sizeTarget (pygbe.classes.Surface attribute)
sortPoints() (in module pygbe.tree.FMMutils)
sortSource (pygbe.classes.Surface attribute)
sortTarget (pygbe.classes.Surface attribute)
source (pygbe.tree.FMMutils.Cell attribute)
split_cell() (in module pygbe.tree.FMMutils)
surf_type (pygbe.classes.Surface attribute)
Surface (class in pygbe.classes)
synchronize() (pygbe.classes.Event method)
T
target (pygbe.tree.FMMutils.Cell attribute)
theta (pygbe.classes.Parameters attribute)
threshold (pygbe.classes.Parameters attribute)
time_an (pygbe.classes.Timing attribute)
time_M2M (pygbe.classes.Timing attribute)
time_M2P (pygbe.classes.Timing attribute)
time_mass (pygbe.classes.Timing attribute)
time_P2M (pygbe.classes.Timing attribute)
time_P2P (pygbe.classes.Timing attribute)
time_sort (pygbe.classes.Timing attribute)
time_till() (pygbe.classes.Event method)
time_trans (pygbe.classes.Timing attribute)
Timing (class in pygbe.classes)
tol (pygbe.classes.Parameters attribute)
tree (pygbe.classes.Surface attribute)
triangle (pygbe.classes.Surface attribute)
triangleSort (pygbe.classes.Surface attribute)
twig (pygbe.classes.Surface attribute)
twig_array (pygbe.tree.FMMutils.Cell attribute)
two_sphere() (in module pygbe.util.an_solution)
U
unsort (pygbe.classes.Surface attribute)
upwardSweep() (in module pygbe.tree.FMMutils)
V
vertex (pygbe.classes.Surface attribute)
vertexDev (pygbe.classes.Surface attribute)
W
wk (pygbe.classes.Surface attribute)
wkDev (pygbe.classes.Surface attribute)
write() (pygbe.main.Logger method)
Wsk (pygbe.classes.Surface attribute)
WskDev (pygbe.classes.Surface attribute)
X
xc (pygbe.tree.FMMutils.Cell attribute)
xcDev (pygbe.classes.Surface attribute)
xcSort (pygbe.classes.Surface attribute)
xi (pygbe.classes.Surface attribute)
xiDev (pygbe.classes.Surface attribute)
XinK (pygbe.classes.Surface attribute)
XinV (pygbe.classes.Surface attribute)
xiSort (pygbe.classes.Surface attribute)
xj (pygbe.classes.Surface attribute)
xjDev (pygbe.classes.Surface attribute)
xjSort (pygbe.classes.Surface attribute)
xk (pygbe.classes.Surface attribute)
xkDev (pygbe.classes.Surface attribute)
Xout_ext (pygbe.classes.Surface attribute)
Xout_int (pygbe.classes.Surface attribute)
xq (pygbe.classes.Field attribute)
xq_gpu (pygbe.classes.Field attribute)
Xsk (pygbe.classes.Surface attribute)
XskDev (pygbe.classes.Surface attribute)
Y
yc (pygbe.tree.FMMutils.Cell attribute)
ycDev (pygbe.classes.Surface attribute)
ycSort (pygbe.classes.Surface attribute)
yi (pygbe.classes.Surface attribute)
yiDev (pygbe.classes.Surface attribute)
yiSort (pygbe.classes.Surface attribute)
yj (pygbe.classes.Surface attribute)
yjDev (pygbe.classes.Surface attribute)
yjSort (pygbe.classes.Surface attribute)
yq_gpu (pygbe.classes.Field attribute)
Z
zc (pygbe.tree.FMMutils.Cell attribute)
zcDev (pygbe.classes.Surface attribute)
zcSort (pygbe.classes.Surface attribute)
zero_areas() (pygbe.classes.Surface method)
zi (pygbe.classes.Surface attribute)
ziDev (pygbe.classes.Surface attribute)
ziSort (pygbe.classes.Surface attribute)
zj (pygbe.classes.Surface attribute)
zjDev (pygbe.classes.Surface attribute)
zjSort (pygbe.classes.Surface attribute)
zq_gpu (pygbe.classes.Field attribute)
PyGBe
Python, GPUs and Boundary elements for biomolecular electrostatics
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