def run(iprec, ifpot, iffld, ifcharge, ifdipole, ifpottarg, iffldtarg,
pos_src, nsources, charge_src, vel_src, dipstr_src, dipvec_src, pot_src, field_src, mass_src,
pos_targ, ntargets, vel_targ, pot_targ, field_targ, mass_targ, nthreads,
times, dt, nsteps, d_pos_src, d_vel_src, d_pos_targ, d_vel_targ, d_pot_src, d_field_src,
ifdirect, iffmm, iffm_multi, d_pot_targ, d_field_targ, tfmm, tdirect,
ifpotsrc_far, ifpotsrc_near,
ifpottarg_far, ifpottarg_near,
iffldsrc_far, iffldsrc_near,
iffldtarg_far, iffldtarg_near,
pot_far_src, pot_near_src,
pot_far_targ, pot_near_targ,
field_far_src, field_near_src,
field_far_targ,field_near_targ,
save, outdir ):
# dealing with the tree structure
ladder = np.zeros( (200,2), dtype=np.dtype('i4')) #200 is the maximum amount of levels
box = np.zeros(20, dtype=np.dtype('i4'))
center_temp = np.zeros(3, dtype=np.dtype('f8'))
corners_temp = np.zeros( (8,3), dtype=np.dtype('f8'))
# arrays for the accelartion for the fmm
accel_src = np.zeros((nsources, 3), dtype=np.dtype('f8'))
accel_targ = np.zeros((ntargets, 3), dtype=np.dtype('f8'))
accel_old_src = np.zeros(accel_src.shape, accel_src.dtype)
accel_old_targ = np.zeros(accel_targ.shape, accel_targ.dtype)
# arrays for the acceleration for the direct solver
d_accel_src = np.zeros(accel_src.shape, accel_src.dtype)
d_accel_old_src = np.zeros(accel_src.shape, accel_src.dtype)
d_accel_targ = np.zeros(accel_targ.shape, accel_targ.dtype)
d_accel_old_targ = np.zeros(accel_targ.shape, accel_targ.dtype)
# this reshaping must be done so that python can use charge to do matrix-vector multiplication later
charge_src_reshape = np.reshape(charge_src, (nsources, 1))
# set some flags
if ifpot == 1 or iffld == 1:
bsource = True
else:
bsource = False
if ifpottarg == 1 or iffldtarg == 1:
btarget = True
else:
btarget = False
# these are the id's of the sources in tree-order (aka box-order)
isource_tree = np.zeros(nsources, dtype=np.dtype('i4'))
itarget_tree = np.zeros(ntargets, dtype=np.dtype('i4'))
# set number of source/ box and set fmm tolerance
nbox = su.set_sources_per_box(iprec, nsources, ntargets) # number of sources per box
epsfmm = su.set_fmm_tolerance(iprec)
ifnear_only = 0
#--------------------------------------------------
# create the tree structure
#--------------------------------------------------
# Could be a problem with when the tree structure is made and how Verlocity Verlet works!
t1 = time.time()
# get the length of the tree structure object for wlists (ntot)
ier, ntot = fortfmm.pre_create_tree(iprec, pos_src, nsources, pos_targ, ntargets, nbox, epsfmm)
# create wlists (it's a workspace)
# wlists_original = np.zeros(ntot, dtype=np.dtype('f8'))
wlists = np.zeros(ntot, dtype=np.dtype('f8'))
# create the tree structure
ier, nlev, nboxes, lused7_original, iisource, iwlists, lwlists, iitarget, size = fortfmm.create_tree(iprec,
pos_src, nsources, pos_targ, ntargets, center_temp, ladder,
wlists, ntot, nbox, epsfmm)
"""
ladder - an integer array dimensioned [nlev, 2], describing the
numbers of boxes on various levels of sybdivision, so that
the first box on level (i) has sequence number laddr[i,1],
and there are laddr[i,2] boxes on level i.
ladder starts counting from level 0
nlev - the maximum level number on which any boxes have
been created. the maximum number possible is 200.
it is recommended that the array laddr above be
dimensioned at least (200,2), in case the user underestimates
the number of levels required.
size: size of the box on level 0
"""
# wlists = np.array(wlists_original, dtype=np.dtype('f8'))
t2 = time.time()
#print "In time it took to create the tree structure: " + str(t2-t1) + " [s]"
# Store information about the tree structure
boxes = np.zeros( (nboxes, 20), dtype=np.dtype('i4'))
centers = np.zeros( (nboxes, 3), dtype=np.dtype('f8'))
corners = np.zeros( (nboxes, 8, 3), dtype=np.dtype('f8'))
# moved the following out of the loop
# these are the id's of the sources in tree-order (aka box-order)
#isource_tree = np.zeros(nsources, dtype=np.dtype('i4'))
#itarget_tree = np.zeros(ntargets, dtype=np.dtype('i4'))
mu.set_boxes(boxes, corners, centers, isource_tree, itarget_tree, wlists, iisource, iitarget, iwlists)
# save the boxes data
# set iter->0 and nsteps->0 (ie setpath(0,0)) to avoid making a new directory
# fpath = os.path.dirname( os.getcwd() ) # this should be /fmmlib3d
fpath = outdir + "/t_0"
#fpath = data_path + "/t_" + str(i)
mu.save_boxes(fpath, boxes, centers, corners, isource_tree, itarget_tree, ladder)
#--------------------------------------------------------------------------------------------------
# finished tree structure
#---------------------------------------------------------------------------------------------------
# Entering time loop
# =========================================================================================
for i in range(nsteps+1): # loop through nsteps + 1 so I can get the velocity for i==nsteps
# set to the original wlists
lused7 = lused7_original
mu.reset_pot_field(iffmm, ifdirect, ifpot, iffld, ifpottarg, iffldtarg,
ifpotsrc_far, ifpotsrc_near,
iffldsrc_far, iffldsrc_near,
ifpottarg_far, ifpottarg_near,
iffldtarg_far, iffldtarg_near,
pot_src, field_src, pot_targ, field_targ,
d_pot_src, d_field_src, d_pot_targ, d_field_targ,
pot_far_src, field_far_src,
pot_near_src, field_near_src,
pot_far_targ, field_far_targ,
pot_near_targ, field_near_targ)
# do the FMM
if (iffmm == 1 or iffm_multi == 1):
t1 = time.time()
ier, lused7 = fortfmm.fmm(iprec, nsources, pos_src, ifcharge, charge_src, ifdipole, dipstr_src, dipvec_src,
ifpot, pot_src, iffld,field_src, ntargets, pos_targ, ifpottarg, pot_targ, iffldtarg, field_targ,
ladder, nlev, nboxes, nbox,
epsfmm, lused7, nthreads, iisource, iwlists, lwlists, iitarget, size, wlists,
ifpotsrc_far, ifpotsrc_near,
iffldsrc_far, iffldsrc_near,
ifpottarg_far, ifpottarg_near,
iffldtarg_far, iffldtarg_near,
ifnear_only,
pot_far_src, field_far_src,
pot_near_src, field_near_src,
pot_far_targ, field_far_targ,
pot_near_targ, field_near_targ)
t2 = time.time()
tfmm[i] = t2 -t1
# sum the far and near field contributions
pot_src = pot_far_src + pot_near_src
pot_targ = pot_far_targ + pot_near_targ
field_src = field_far_src + field_near_src
field_targ = field_far_targ + field_near_targ
# do the direct calculation
if (ifdirect == 1):
#print "\nDoing the direct calculation. nthreads = " + str(nthreads)
t1 = time.time()
fortfmm.direct(d_pos_src, ifcharge,charge_src, ifdipole, dipstr_src, dipvec_src, ifpot, d_pot_src, iffld,
d_field_src, d_pos_targ, ifpottarg, d_pot_targ, iffldtarg, d_field_targ, nthreads)
t2 = time.time()
tdirect[i] = t2 - t1
# calculate the new acceleration
accel_src[:,:] = field_src.real[:,:] * charge_src.real[:]
accel_targ[:,:] = field_targ.real[:,:] * 1.0
# update velocity using FORWARD EULER
mu.forwardEuler(vel_src, accel_src, dt)
mu.forwardEuler(vel_targ, accel_targ, dt)
# update position using FORWARD EULER
mu.forwardEuler(pos_src, vel_src, dt)
mu.forwardEuler(pos_targ, vel_targ, dt)
if save is True:
# set the path
newpath, oldpath = mu.set_path(outdir, i, nsteps)
mu.save_pot_field( oldpath, iffmm, ifdirect, ifpot, iffld, ifpottarg, iffldtarg,
ifpotsrc_far, ifpotsrc_near,
iffldsrc_far, iffldsrc_near,
ifpottarg_far, ifpottarg_near,
iffldtarg_far, iffldtarg_near,
pot_src, pot_targ, field_src, field_targ,
d_pot_src, d_field_src, d_pot_targ, d_field_targ,
pot_far_src, pot_near_src,
field_far_src, field_near_src,
pot_far_targ, field_far_targ,
pot_near_targ, field_near_targ,
accel_src, accel_targ, d_accel_src, d_accel_targ)
# save the velocity (v_n). Do not save velocity for i == 0. Already known.
if i > 0:
mu.save_vel(oldpath, vel_src, vel_targ, d_vel_src, d_vel_targ)
mu.save_pos(oldpath, pos_src, pos_targ, d_pos_src, d_pos_targ)
# =========================================================================================
"""------------------- Outside the time loop. Need to update the velocities ------------------"""
# testing
#printStuff(iisource, iitarget, iwlists, lwlists, lused7, nbox, nboxes, ladder, size, epsfmm, nlev)
if save is True:
# save potentials and fields
mu.save_pot_field( oldpath, iffmm, ifdirect, ifpot, iffld, ifpottarg, iffldtarg,
ifpotsrc_far, ifpotsrc_near,
iffldsrc_far, iffldsrc_near,
ifpottarg_far, ifpottarg_near,
iffldtarg_far, iffldtarg_near,
pot_src, pot_targ, field_src, field_targ,
d_pot_src, d_field_src, d_pot_targ, d_field_targ,
pot_far_src, pot_near_src,
field_far_src, field_near_src,
pot_far_targ, field_far_targ,
pot_near_targ, field_near_targ,
accel_src, accel_targ, d_accel_src, d_accel_targ)
return ier, nlev, nboxes, nbox, lused7
def fmm_run(
iprec,
ifpot,
iffld,
ifcharge,
ifdipole,
ifpottarg,
iffldtarg,
pos_src,
nsources,
charge_src,
dipstr_src,
dipvec_src,
pot_src,
field_src,
pos_targ,
ntargets,
pot_targ,
field_targ,
nthreads,
nbox,
epsfmm,
ifpotsrc_far,
ifpotsrc_near,
iffldsrc_far,
iffldsrc_near,
ifpottarg_far,
ifpottarg_near,
iffldtarg_far,
iffldtarg_near,
ifnear_only,
pot_far_src,
field_far_src,
pot_near_src,
field_near_src,
pot_far_targ,
field_far_targ,
pot_near_targ,
field_near_targ,
):
# dealing with the tree structure
ladder = np.zeros((200, 2), dtype=np.dtype("i4")) # 200 is the maximum amount of levels
box = np.zeros(20, dtype=np.dtype("i4"))
center_temp = np.zeros(3, dtype=np.dtype("f8"))
corners_temp = np.zeros((8, 3), dtype=np.dtype("f8"))
# this reshaping must be done so that python can use charge to do matrix-vector multiplication later
charge_src_reshape = np.reshape(charge_src, (nsources, 1))
# these are the id's of the sources in tree-order (aka box-order)
isource_tree = np.zeros(nsources, dtype=np.dtype("i4"))
itarget_tree = np.zeros(ntargets, dtype=np.dtype("i4"))
# --------------------------------------------------
# create the tree structure
# --------------------------------------------------
# get the length of the tree structure object for wlists (ntot)
ier, ntot = fortfmm.pre_create_tree(iprec, pos_src, nsources, pos_targ, ntargets, nbox, epsfmm)
# create wlists (it's a workspace)
# wlists_original = np.zeros(ntot, dtype=np.dtype('f8'))
wlists = np.zeros(ntot, dtype=np.dtype("f8"))
# create the tree structure
ier, nlev, nboxes, lused7_original, iisource, iwlists, lwlists, iitarget, size = fortfmm.create_tree(
iprec, pos_src, nsources, pos_targ, ntargets, center_temp, ladder, wlists, ntot, nbox, epsfmm
)
"""
ladder - an integer array dimensioned [nlev, 2], describing the
numbers of boxes on various levels of sybdivision, so that
the first box on level (i) has sequence number laddr[i,1],
and there are laddr[i,2] boxes on level i.
ladder starts counting from level 0
nlev - the maximum level number on which any boxes have
been created. the maximum number possible is 200.
it is recommended that the array laddr above be
dimensioned at least (200,2), in case the user underestimates
the number of levels required.
size: size of the box on level 0
"""
# wlists = np.array(wlists_original, dtype=np.dtype('f8'))
# Store information about the tree structure
boxes = np.zeros((nboxes, 20), dtype=np.dtype("i4"))
centers = np.zeros((nboxes, 3), dtype=np.dtype("f8"))
corners = np.zeros((nboxes, 8, 3), dtype=np.dtype("f8"))
mu.set_boxes(boxes, corners, centers, isource_tree, itarget_tree, wlists, iisource, iitarget, iwlists)
# save the boxes data
# set iter->0 and nsteps->0 (ie setpath(0,0)) to avoid making a new directory
# fpath = os.path.dirname( os.getcwd() ) # this should be /fmmlib3d
# fpath = fpath + "/mydata/t_0/"
# --------------------------------------------------------------------------------------------------
# finished tree structure
# ---------------------------------------------------------------------------------------------------
# set to the original wlists
lused7 = lused7_original
ier, lused7 = fortfmm.fmm(
iprec,
nsources,
pos_src,
ifcharge,
charge_src,
ifdipole,
dipstr_src,
dipvec_src,
ifpot,
pot_src,
iffld,
field_src,
ntargets,
pos_targ,
ifpottarg,
pot_targ,
iffldtarg,
field_targ,
ladder,
nlev,
nboxes,
nbox,
epsfmm,
lused7,
nthreads,
iisource,
iwlists,
lwlists,
iitarget,
size,
wlists,
ifpotsrc_far,
ifpotsrc_near,
iffldsrc_far,
iffldsrc_near,
ifpottarg_far,
ifpottarg_near,
iffldtarg_far,
iffldtarg_near,
ifnear_only,
pot_far_src,
field_far_src,
pot_near_src,
field_near_src,
pot_far_targ,
field_far_targ,
pot_near_targ,
field_near_targ,
)
return ier, nlev, nboxes, nbox, lused7