def runspbertha(pberthaopt):
sys.path.insert(0, pberthaopt.berthamodpath)
import berthamod
print("Options: ")
for att in [a for a in dir(pberthaopt) if not a.startswith('__')]:
print(att, " = ", getattr(pberthaopt, att))
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
print("SO File ", pberthaopt.wrapperso, " does not exist")
exit(1)
verbosity = pberthaopt.verbosity
dumpfiles = int(pberthaopt.dumpfiles)
bertha = berthamod.pybertha(pberthaopt.wrapperso)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
start = time.time()
cstart = time.process_time()
ovapm, eigemfirst, fockm, eigen = bertha.run()
end = time.time()
cend = time.process_time()
print("Totaltime: ", end - start, " (CPU time: ", cend - cstart, ") s ")
print("MainRun Time: ", bertha.get_mainruntime() , \
" (CPU time: " , bertha.get_mainrunctime(), ") s ")
sys.stdout.flush()
if (fockm is None) or (eigen is None) or (fockm is None) \
or (eigen is None):
print("Error in bertha run")
exit(-1)
print("")
print("Final results ")
for i in range(nocc + nopen):
print("eigenvalue %5d %20.8f" % (i + 1, eigen[i + nshift] - sfact))
print(" lumo %20.8f" % (eigen[i + nshift + 1]))
erep = bertha.get_erep()
etotal = bertha.get_etotal()
ecoul = bertha.get_eecoul()
exc = bertha.get_eexc()
print("")
print("total electronic energy = %30.15f" % (etotal - (sfact * nocc)))
print("nuclear repulsion energy = %30.15f" % (erep))
print("total energy = %30.15f" % (etotal + erep -
(sfact * nocc)))
print("coulomb energy = %30.15f" % (ecoul))
print("Exc energy = %30.15f" % (exc))
bertha.finalize()
print("\n\nSTART second RUN \n\n")
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
start = time.time()
cstart = time.process_time()
ovapm, eigem, fockm, eigen = bertha.run(eigemfirst)
end = time.time()
cend = time.process_time()
print("Totaltime: ", end - start, " (CPU time: ", cend - cstart, ") s ")
print("MainRun Time: ", bertha.get_mainruntime() , \
" (CPU time: " , bertha.get_mainrunctime(), ") s ")
sys.stdout.flush()
if (fockm is None) or (eigen is None) or (fockm is None) \
or (eigen is None):
print("Error in bertha run")
exit(-1)
print("")
print("Final results ")
for i in range(nocc + nopen):
print("eigenvalue %5d %20.8f" % (i + 1, eigen[i + nshift] - sfact))
print(" lumo %20.8f" % (eigen[i + nshift + 1]))
erep = bertha.get_erep()
etotal = bertha.get_etotal()
ecoul = bertha.get_eecoul()
exc = bertha.get_eexc()
print("")
print("total electronic energy = %30.15f" % (etotal - (sfact * nocc)))
print("nuclear repulsion energy = %30.15f" % (erep))
print("total energy = %30.15f" % (etotal + erep -
(sfact * nocc)))
print("coulomb energy = %30.15f" % (ecoul))
print("Exc energy = %30.15f" % (exc))
bertha.finalize()
def normal_run(args):
print("Options: ")
print(args)
print("")
print("")
if not os.path.isfile(args.wrapperso):
print("SO File ", args.wrapperso, " does not exist")
return False
bertha = berthamod.pybertha(args.wrapperso)
ovapm, eigem, fockm, eigen = single_point (args, bertha)
if ovapm is None:
return False
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
bertha.realtime_init()
print("Start RT")
debug = args.debug
dt = args.dt
t_int = args.totaltime
niter = int(t_int/dt)
print("Debug: ", debug)
print("dt : ", dt)
print("Total time : ", t_int)
print("Number of iterations: ", niter)
sys.stdout.flush()
ene_list = []
dip_list = []
weight_list = []
imp_list = []
Enuc_list = []
C = eigem
D_0 = numpy.zeros((ndim,ndim), dtype=numpy.complex128)
for num in range(nocc):
D_0[num+nshift,num+nshift]=1.0+0.0j
fo = sys.stderr
if debug:
fo = open("debug_info.txt", "w")
#print type(eigem)
#C_inv used to backtransform D(AO)
try:
C_inv = numpy.linalg.inv(eigem)
except LinAlgError:
print("Error in numpy.linalg.inv of eigem")
return False
if debug:
test = numpy.matmul(C_inv, eigem)
fo.write("Check if atol is 1.e-14 for inversion of C: %s\n"% \
numpy.allclose(numpy.eye((ndim),dtype=numpy.complex128), \
test,atol=1.e-14))
if debug:
diff = test - numpy.eye((ndim),dtype=numpy.complex128)
mdiff = numpy.max(diff)
fo.write(" maxdiff is: %.12e %.12e\n"%(mdiff.real, mdiff.imag))
if debug:
test = numpy.matmul(numpy.conjugate(C.T),numpy.matmul(ovapm,C))
fo.write("Check orthonormal orbitals (atol = 1.e-14): %s\n"% \
numpy.allclose(numpy.eye((ndim),dtype=numpy.complex128), \
test, atol=1.e-14))
diff = test - numpy.eye((ndim),dtype=numpy.complex128)
mdiff = numpy.max(diff)
fo.write(" maxdiff is: %.12e %.12e\n"%(mdiff.real, mdiff.imag))
#build density in ao basis
occeigv = numpy.zeros((ndim,nocc), dtype=numpy.complex128)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da = numpy.matmul(occeigv,numpy.conjugate(occeigv.transpose()))
print("")
print("Dump ground state density density0.cube")
bertha.density_to_cube(Da.T, "density0.cube",margin=5.0)
print("Done")
if debug:
#check trace(S Da)
trace_ds = numpy.trace(numpy.matmul(Da,ovapm))
trace_dsfock = numpy.trace(numpy.matmul(Da,fockm))
fo.write("Density matrix trace at t0: %.12e %.12e \n"%(trace_ds.real,trace_ds.imag))
fo.write("Trace of fock*density at t0: %.12e %.12e \n"%(trace_dsfock.real, trace_dsfock.imag))
normalise = 1
dip_mat = None
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
if (args.direction == 4):
dip_mat = dipx_mat
elif (args.direction == 3):
dip_mat = dipy_mat
elif (args.direction == 2):
dip_mat = dipz_mat
if debug:
fockmh = numpy.conjugate(fockm.T)
diff_fockmh = fockm-fockmh
mdiff = numpy.max(diff_fockmh)
fo.write("Check max diff fockm-fockmh: %.12e %.12e\n"%\
(mdiff.real, mdiff.imag))
fo.write("Fockm (t=0) is hermitian: %s \n"%numpy.allclose(fockm,fockmh,atol=1.e-15))
molist = args.select.split("&")
occlist = molist[0].split(";")
occlist = [int(m) for m in occlist]
virtlist = molist[1].split(";")
virtlist = [int(m) for m in virtlist]
if (args.pulse == "analytic"):
Amp=args.pulseFmax
# to check
dipz_mo=numpy.matmul(numpy.conjugate(C.T),numpy.matmul(dip_mat,C))
if args.select_pert:
dipz_mo=rtutil.dipole_selection(dipz_mo,nshift,nocc,occlist,virtlist,fo,debug)
print(" Perturb with analytic kick ")
u0=rtutil.exp_opmat(dipz_mo,numpy.float_(-Amp),debug,fo)
Dp_init=numpy.matmul(u0,numpy.matmul(D_0,numpy.conjugate(u0.T)))
#transform back Dp_int
Da=numpy.matmul(C,numpy.matmul(Dp_init,numpy.conjugate(C.T)))
D_0=Dp_init
print("Start first mo_fock_mid_forwd_eval ")
fock_mid_init = rtutil.mo_fock_mid_forwd_eval(bertha,Da,fockm,0,numpy.float_(dt),\
dip_mat,C,C_inv,ovapm,ndim, debug, fo, args.pulse, args.pulseFmax, args.pulsew, args.t0, args.pulseS,
args.propthresh)
if (fock_mid_init is None):
print("Error accurs in mo_fock_mid_forwd_eval")
return False
if debug:
fock_mid_h=numpy.conjugate(fock_mid_init.T)
diff_fock_mid_h=fock_mid_init-fock_mid_h
fo.write("Max diff fock_mid_init-fock_mid_h"%(numpy.max(diff_fock_mid_h)))
fo.write('Fockm (t=1/2) is hermitian: %s\n'%
numpy.allclose(fock_mid_init,fock_mid_h,atol=1.e-14))
fockp_mid_init=numpy.matmul(numpy.conjugate(C.T),numpy.matmul(fock_mid_init,C))
u=rtutil.exp_opmat(fockp_mid_init,numpy.float_(dt),debug,fo)
#u=rtutil.exp_opmat(fockp_mid_init,numpy.float_(dt),debug,fo)
#u=scila.expm(-1.j*fockp_mid_init*dt)
temp=numpy.matmul(D_0,numpy.conjugate(u.T))
Dp_t1=numpy.matmul(u,temp)
#check u if unitary
if debug:
test_u=numpy.matmul(u,numpy.conjugate(u.T))
fo.write('U is unitary : %s' %
numpy.allclose(test_u,numpy.eye(u.shape[0]),atol=1.e-14))
#backtrasform Dp_t1
D_t1=numpy.matmul(C,numpy.matmul(Dp_t1,numpy.conjugate(C.T)))
if debug:
diff = D_t1 - Da
mdiff = numpy.max(diff)
fo.write("Max diff density: %.12e %.12e \n"%(mdiff.real, mdiff.imag))
dip_list.append(numpy.trace(numpy.matmul(Da,dip_mat)))
dip_list.append(numpy.trace(numpy.matmul(D_t1,dip_mat)))
if (args.pulse == "analytic"):
if (occlist[0] != -2):
#dipoleanalysis
res=rtutil.dipoleanalysis(dipz_mo,D_0,occlist,virtlist,nshift,fo,debug)
weight_list.append(res)
res=rtutil.dipoleanalysis(dipz_mo,Dp_t1,occlist,virtlist,nshift,fo,debug)
weight_list.append(res)
if debug:
fo.write("Dipole: %.12e\n"%(numpy.trace(numpy.matmul(Da,dip_mat))).real)
fo.write("Dipole: %.12e\n"%(numpy.trace(numpy.matmul(D_t1,dip_mat))).real)
if debug:
tfock = numpy.trace(numpy.matmul(D_t1,fockm))
fo.write("Trace fock*density t1: %.12e, %.12e\n"%(tfock.real, tfock.imag))
trace_ds=numpy.trace(numpy.matmul(D_t1,ovapm))
fo.write(" Traceds: %.12e %.12ei\n" % (trace_ds.real,trace_ds.imag))
Ndip_z=0.0
#estrarre le 3 componenti del dipolo nucleare
D_ti=D_t1
Dp_ti=Dp_t1
#aggiungere repulsione nucleare
#Enuc_list.append(-func_t0*Ndip_z+Nuc_rep) #just in case of non-zero nuclear dipole
start = time.time()
cstart = time.process_time()
fockm_ti=bertha.get_realtime_fock(D_ti.T)
end = time.time()
cend = time.process_time()
print("RealTime Fock Time: %15.5f"%(end-start), " (CPU: %15.5f"%(cend-cstart), " ) s")
print("RealTime Fock Time Without Py: %15.5f"%(bertha.get_focktime()), \
" (CPU: %15.5f"%(bertha.get_fockctime()), " ) s")
print("")
ene_list.append(numpy.trace(numpy.matmul(Da,fockm)))
ene_list.append(numpy.trace(numpy.matmul(D_ti,fockm_ti)))
print("Starting iterations ...")
print("")
fock_mid_backwd = numpy.copy(fock_mid_init)
return run_iterations_from_to (1, niter, bertha, args, fock_mid_backwd, \
dt, dip_mat, C, C_inv, ovapm, ndim, debug, Dp_ti, dip_list, ene_list, \
weight_list, fo, D_ti, occlist)
def runspberthaembedrt(pberthaopt):
sys.path.insert(0, pberthaopt.berthamodpath)
import berthamod
print("Options: ")
for att in [a for a in dir(pberthaopt) if not a.startswith('__')]:
print(att, " = ", getattr(pberthaopt, att))
print("")
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
print("SO File ", pberthaopt.wrapperso, " does not exist")
exit(1)
bertha = berthamod.pybertha(pberthaopt.wrapperso)
fittcoefffname = pberthaopt.fitcoefffile
vctfilename = pberthaopt.vctfile
ovapfilename = pberthaopt.ovapfile
fnameinput = pberthaopt.inputfile
if not os.path.isfile(fnameinput):
print("File ", fnameinput, " does not exist")
exit(1)
fittfname = pberthaopt.fittfile
if not os.path.isfile(fittfname):
print("File ", fittfname, " does not exist")
exit(1)
verbosity = pberthaopt.verbosity
dumpfiles = int(pberthaopt.dumpfiles)
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
#generate a sample grid
"""
npoints = 10
grid = numpy.zeros((npoints, 4))
grid = numpy.ascontiguousarray(grid, dtype=numpy.double)
pot = numpy.zeros(npoints)
pot = numpy.ascontiguousarray(pot, dtype=numpy.double)
x = -1.0
y = -100.0
z = -1000.0
w = 1.0
for i in range(npoints):
grid[i,0] = x
grid[i,1] = y
grid[i,2] = z
grid[i,3] = w
pot[i] = x*y*z*w
x += 1.0
y += 1.0
z += 1.0
w += 0.1
"""
#read a real grid
grid = berthamod.read_grid_file("ADFGRID")
if grid is None:
print("ERROR in reading gridfile")
exit(1)
grid, pot = berthamod.read_grid_ampot_file("EMBPOT_PYEMBED_ADFGRID_H2O")
if grid is None or pot is None:
print("ERROR in reading gridpotfile")
exit(1)
npoints = grid.shape[0]
start = time.time()
cstart = time.process_time()
print("Type grid", type(grid), grid.shape)
print("Type pot", type(pot), pot.shape)
bertha.set_embpot_on_grid(grid, pot)
print("Type pot", pot)
#main run here
ovapm, eigem, fockm, eigen = bertha.run()
density = bertha.get_density_on_grid(grid)
# TEST density on grid
# print("TEST density on grid")
# print("Type density", type(density), density.shape)
# print("Scalar product" , "density.weigt", numpy.dot(density,grid[:,3]))
# print("Dip x" , "density.weigt", numpy.dot(density*grid[:,3],grid[:,0]))
# print("Dip y" , "density.weigt", numpy.dot(density*grid[:,3],grid[:,1]))
# print("Dip z" , "density.weigt", numpy.dot(density*grid[:,3],grid[:,2]))
"""
for i in range(npoints):
val = grid[i,0] * grid[i,1] * grid[i,2] * grid[i,3]
print("Python L: %15.5f vs %15.5f"%(density[i], val))
"""
end = time.time()
cend = time.process_time()
print("Totaltime: ", end - start, " (CPU time: ", cend - cstart, ") s ")
print("MainRun Time: ", bertha.get_mainruntime() , \
" (CPU time: ", bertha.get_mainrunctime(), ") s ")
bertha.realtime_init()
normalise = 1
dip_mat = None
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da = numpy.matmul(occeigv, numpy.conjugate(occeigv.transpose()))
dipx_ref = numpy.trace(numpy.matmul(Da, dipx_mat)).real
dipy_ref = numpy.trace(numpy.matmul(Da, dipy_mat)).real
dipz_ref = numpy.trace(numpy.matmul(Da, dipz_mat)).real
print("Dipx ", dipx_ref)
print("Dipy ", dipy_ref)
print("Dipz ", dipz_ref)
# TEST density on grid
bertha.finalize()
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
field = 0.00001
pot = grid[:, 0] * field
bertha.set_embpot_on_grid(grid, pot)
ovapm, eigem, fockm, eigen = bertha.run()
etotal1 = bertha.get_etotal()
bertha.finalize()
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
pot = grid[:, 0] * (-field)
bertha.set_embpot_on_grid(grid, pot)
ovapm, eigem, fockm, eigen = bertha.run()
etotal2 = bertha.get_etotal()
dipx = (etotal2 - etotal1) / (2 * field)
print("Dipole moment analitical: Tr(D dip_mat)")
print("Dip x ", dipx_ref)
print("Dip y ", dipy_ref)
print("Dip z ", dipz_ref)
print("TEST dipole moment from density on grid numerical integration")
print(" ")
print("Type density", type(density), density.shape)
print("Scalar product", "density.weigt", numpy.dot(density, grid[:, 3]))
print("Dip x", "density.weigt", numpy.dot(density * grid[:, 3], grid[:,
0]))
print("Dip y", "density.weigt", numpy.dot(density * grid[:, 3], grid[:,
1]))
print("Dip z", "density.weigt", numpy.dot(density * grid[:, 3], grid[:,
2]))
print(" ")
print("TEST one electron potential (embedding) in g-spinor")
print("Potential used -x*E and x*E evaluating dipole via finite field")
print("Dip x", "from finite field", dipx)
sys.stdout.flush()
help="cube margin parameter (default = 10.0)",
required=False,
type=numpy.float64,
default=10.0)
args = parser.parse_args()
print("Options: ")
print(args)
print("")
print("")
if not os.path.isfile(args.wrapperso):
print("SO File ", args.wrapperso, " does not exist")
exit(1)
bertha = berthamod.pybertha(args.wrapperso)
fittcoefffname = args.fitcoefffile
vctfilename = args.vctfile
ovapfilename = args.ovapfile
fnameinput = args.inputfile
if not os.path.isfile(fnameinput):
print("File ", fnameinput, " does not exist")
exit(1)
fittfname = args.fittfile
if not os.path.isfile(fittfname):
print("File ", fittfname, " does not exist")
exit(1)
def restart_run(args):
fp = open(args.restartfile, 'r')
json_data = json.load(fp)
fp.close()
jstart = int(json_data["j"])
ndim = int(json_data["ndim"])
niter = int(json_data["niter"])
fock_mid_backwd_REAL = numpy.float_(json_data["fock_mid_backwd_REAL"])
fock_mid_backwd_IMAG = numpy.float_(json_data["fock_mid_backwd_IMAG"])
dip_mat_REAL = numpy.float_(json_data["dip_mat_REAL"])
dip_mat_IMAG = numpy.float_(json_data["dip_mat_IMAG"])
C_REAL = numpy.float_(json_data["C_REAL"])
C_IMAG = numpy.float_(json_data["C_IMAG"])
C_inv_REAL = numpy.float_(json_data["C_inv_REAL"])
C_inv_IMAG = numpy.float_(json_data["C_inv_IMAG"])
ovapm_REAL = numpy.float_(json_data["ovapm_REAL"])
ovapm_IMAG = numpy.float_(json_data["ovapm_IMAG"])
Dp_ti_REAL = numpy.float_(json_data["Dp_ti_REAL"])
Dp_ti_IMAG = numpy.float_(json_data["Dp_ti_IMAG"])
D_ti_REAL = numpy.float_(json_data["D_ti_REAL"])
D_ti_IMAG = numpy.float_(json_data["D_ti_IMAG"])
fock_mid_backwd = check_and_covert (fock_mid_backwd_REAL ,
fock_mid_backwd_IMAG, ndim)
dip_mat = check_and_covert (dip_mat_REAL, dip_mat_IMAG, ndim)
C = check_and_covert (C_REAL, C_IMAG, ndim)
C_inv = check_and_covert (C_inv_REAL, C_inv_IMAG, ndim)
ovapm = check_and_covert (ovapm_REAL, ovapm_IMAG, ndim)
Dp_ti = check_and_covert (Dp_ti_REAL, Dp_ti_IMAG, ndim)
D_ti = check_and_covert (D_ti_REAL, D_ti_IMAG, ndim)
ene_list_REAL = numpy.float_(json_data["ene_list_REAL"])
ene_list_IMAG = numpy.float_(json_data["ene_list_IMAG"])
dip_list_REAL = numpy.float_(json_data["dip_list_REAL"])
dip_list_IMAG = numpy.float_(json_data["dip_list_IMAG"])
if ((ene_list_REAL.shape != ene_list_IMAG.shape) or
(dip_list_REAL.shape != dip_list_IMAG.shape) or
(ene_list_REAL.shape != dip_list_IMAG.shape)):
return False
ene_list = []
dip_list = []
for i in range(ene_list_REAL.shape[0]):
ene_list.append(numpy.complex128(complex(ene_list_REAL[i],
ene_list_IMAG[i])))
dip_list.append(numpy.complex128(complex(dip_list_REAL[i],
dip_list_IMAG[i])))
weight_list_REAL = numpy.float_(json_data["weight_list_REAL"])
weight_list_IMAG = numpy.float_(json_data["weight_list_IMAG"])
weight_list = []
if len(weight_list_REAL) != len(weight_list_IMAG):
print("ERROR in weight_list size")
exit(1)
for i in range(len(weight_list_REAL)):
if len(weight_list_REAL[i]) != len(weight_list_IMAG[i]):
print("ERROR in weight_list size")
exit(1)
row = numpy.zeros(len(weight_list_REAL[i]), dtype=numpy.complex128)
for j in range(len(weight_list_REAL[i])):
row[j] = numpy.complex128(complex(weight_list_REAL[i][j],
weight_list_IMAG[i][j]))
weight_list.append(row)
args.pulse = json_data['pulse']
args.pulseFmax = json_data['pulseFmax']
args.pulsew = json_data['pulsew']
args.dt = json_data['dt']
args.inputfile = json_data['inputfile']
args.fittfile = json_data["fittfile"]
args.fitcoefffile = json_data["fitcoefffile"]
args.vctfile = json_data["vctfile"]
args.ovapfile = json_data["ovapfile"]
args.dumpfiles = json_data["dumpfiles"]
args.direction = json_data["direction"]
totaltime = json_data["totaltime"]
if args.totaltime < totaltime:
args.totaltime = json_data["totaltime"]
else:
niter = int(args.totaltime/args.dt)
args.debug = json_data["debug"]
args.verbosity = json_data["verbosity"]
args.iterations = json_data["iterations"]
args.select = json_data["select"]
args.select_pert = json_data["select_pert"]
args.propthresh = json_data["propthresh"]
args.thresh = json_data["thresh"]
args.wrapperso = json_data["wrapperso"]
args.dumprestartnum = json_data["dumprestartnum"]
args.pulseS = json_data["pulseS"]
args.t0 = json_data["t0"]
molist = args.select.split("&")
occlist = molist[0].split(";")
occlist = [int(m) for m in occlist]
virtlist = molist[1].split(";")
virtlist = [int(m) for m in virtlist]
print("Options: ")
print(args)
print("")
print("")
if not os.path.isfile(args.wrapperso):
print("SO File ", args.wrapperso, " does not exist")
return False
bertha = berthamod.pybertha(args.wrapperso)
# TODO to remove full run
ovapm, eigem, fockm, eigen = single_point (args, bertha)
if ovapm is None:
return False
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
bertha.realtime_init()
print("Start RT")
debug = args.debug
dt = args.dt
t_int = args.totaltime
print("Debug: ", debug)
print("dt : ", dt)
print("Total time : ", t_int)
print("Number of iterations: ", niter)
sys.stdout.flush()
fo = sys.stderr
if debug:
fo = open("debug_info.txt", "w")
return run_iterations_from_to (jstart+1, niter, bertha, args, fock_mid_backwd, \
dt, dip_mat, C, C_inv, ovapm, ndim, debug, Dp_ti, dip_list, ene_list, \
weight_list, fo, D_ti, occlist)
def runspbertha(pberthaopt):
sys.path.insert(0, pberthaopt.berthamodpath)
import berthamod
#import os, psutil
#process = psutil.Process(os.getpid())
#print(process.memory_info()) # in bytes
print("Options: ")
for att in [a for a in dir(pberthaopt) if not a.startswith('__')]:
print(att, " = ", getattr(pberthaopt, att))
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
print("SO File ", pberthaopt.wrapperso, " does not exist")
exit(1)
bertha = berthamod.pybertha(pberthaopt.wrapperso)
fittcoefffname = pberthaopt.fitcoefffile
vctfilename = pberthaopt.vctfile
ovapfilename = pberthaopt.ovapfile
fnameinput = pberthaopt.inputfile
if not os.path.isfile(fnameinput):
print("File ", fnameinput, " does not exist")
exit(1)
fittfname = pberthaopt.fittfile
if not os.path.isfile(fittfname):
print("File ", fittfname, " does not exist")
exit(1)
verbosity = pberthaopt.verbosity
dumpfiles = int(pberthaopt.dumpfiles)
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(0)
bertha.init()
#print(process.memory_info()) # in bytes
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
start = time.time()
cstart = time.process_time()
#print(process.memory_info()) # in bytes
if pberthaopt.gridfilename != "" and \
pberthaopt.potfilename != "":
if os.path.isfile(pberthaopt.gridfilename) and \
os.path.isfile(pberthaopt.potfilename):
grid = berthamod.read_sgrid_file(pberthaopt.gridfilename)
pot = berthamod.read_pot_file(pberthaopt.potfilename)
if (pot is not None) and (grid is not None):
if grid.shape[0] == pot.shape[0]:
bertha.set_embpot_on_grid(grid, pot)
else:
print("ERROR: grid and pot files are not compatible")
exit(1)
else:
print("ERROR: " + pberthaopt.gridfilename + " and/or " +
pberthaopt.potfilename + " do not exist")
exit(1)
ovapm, eigem, fockm, eigen = bertha.run()
end = time.time()
cend = time.process_time()
print("Totaltime: ", end - start, " (CPU time: ", cend - cstart, ") s ")
print("MainRun Time: ", bertha.get_mainruntime() , \
" (CPU time: " , bertha.get_mainrunctime(), ") s ")
sys.stdout.flush()
if (fockm is None) or (eigen is None) or (fockm is None) \
or (eigen is None):
print("Error in bertha run")
exit(-1)
"""
counter = 0
for i in range(ndim):
print "i ==> ", i+1, eigen[i]
for j in range(ndim):
sys.stdout.write("(%20.10f %20.10fi) \n"%(
eigenvctbu[counter], eigenvctbu[counter+1]))
counter = counter + 2
print ""
"""
print("")
print("Final results ")
for i in range(nocc + nopen):
print("eigenvalue %5d %20.8f" % (i + 1, eigen[i + nshift] - sfact))
print(" lumo %20.8f" % (eigen[i + nshift + 1]))
erep = bertha.get_erep()
etotal = bertha.get_etotal()
ecoul = bertha.get_eecoul()
exc = bertha.get_eexc()
print("")
print("total electronic energy = %30.15f" % (etotal - (sfact * nocc)))
print("nuclear repulsion energy = %30.15f" % (erep))
print("total energy = %30.15f" % (etotal + erep -
(sfact * nocc)))
print("coulomb energy = %30.15f" % (ecoul))
print("Exc energy = %30.15f" % (exc))
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
etotal = etotal + erep - (sfact * nocc)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
if pberthaopt.eda_nocv_info:
encoder.FLOAT_REPR = lambda o: format(o, '.25E')
json_data = get_json_data(pberthaopt, etotal, erep, ecoul, exc, ndim,
nocc, occeigv)
with open(pberthaopt.eda_nocv_frag_file, 'w') as fp:
json.dump(json_data, fp, sort_keys=True, indent=4)
"""
for i in range(nocc):
print "i ==> ", i+1, eigen[i+nshift]
for j in range(ndim):
sys.stdout.write("(%20.10f %20.10fi)\n"%(
occeigv[j, i].real, occeigv[j, i].imag))
print ""
"""
print("")
print("Compute density matrix ")
density = numpy.matmul(occeigv,
numpy.conjugate(occeigv.transpose()),
out=None)
density = numpy.matmul(density, ovapm)
print("Trace ")
trace = density.trace()
print("(%20.10f, %20.10fi)" % (trace.real, trace.imag))
drx = pberthaopt.deltax
dry = pberthaopt.deltay
drz = pberthaopt.deltaz
margin = pberthaopt.lmargin
if (pberthaopt.cube == True):
bertha.density_to_cube((density).T, "density.cube", margin, drx, dry,
drz)
if (pberthaopt.cubebox == True):
bertha.density_to_cube_limit((density).T, "densitybox.cube", \
(pberthaopt.xmin, pberthaopt.ymin, \
pberthaopt.zmin), (pberthaopt.xmax, \
pberthaopt.ymax, pberthaopt.zmax), \
drx, dry, drz )
bertha.realtime_init()
normalise = 1
numofatom = bertha.get_natoms()
print("Num of atoms: ", numofatom)
for i in range(numofatom):
print(bertha.get_coords(i))
"""
outep = open("eps.txt", "w")
griddim = 50
xmin = 9.0
xmax = 12.0
ymin = 6.0
ymax = 10.0
zmax = 7.0
zmin = -3.0
dx = (xmax - xmin)/float(griddim)
dy = (ymax - ymin)/float(griddim)
x = xmin
for i in range(griddim):
y = ymin
for j in range(griddim):
z = 0.0
eps = bertha.get_eps (x, y, z)
outep.write (" %10.5e %10.5e %10.5e \n"%(x, y, eps))
y = y + dy
x = x + dx
dz = (zmax - zmin)/float(griddim)
z = zmin
for i in range(griddim):
eps = bertha.get_eps (0.0, 0.0, z)
outep.write (" %10.5e %10.5e \n"%(z, eps))
z = z + dz
"""
bertha.finalize()
"""
def runspberthaembed(pberthaopt, restart=False, stdoutprint=True):
ovapm = None
eigem = None
fockm = None
eigen = None
verbosity = -1
verbosity = pberthaopt.verbosity
if not stdoutprint:
verbosity = 0
import berthamod
import pyembmod
if stdoutprint:
print("Options: ")
for att in [a for a in dir(pberthaopt) if not a.startswith('__')]:
print(att, " = ", getattr(pberthaopt, att))
print("")
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
raise Exception("SO File ", pberthaopt.wrapperso, " does not exist")
fittcoefffname = pberthaopt.fitcoefffile
vctfilename = pberthaopt.vctfile
ovapfilename = pberthaopt.ovapfile
fnameinput = pberthaopt.inputfile
if not os.path.isfile(fnameinput):
raise Exception("File ", fnameinput, " does not exist")
fittfname = pberthaopt.fittfile
if not os.path.isfile(fittfname):
raise Exception("File ", fittfname, " does not exist")
dumpfiles = int(pberthaopt.dumpfiles)
static_field = pberthaopt.static_field
fmax = pberthaopt.fmax
fdir = pberthaopt.fdir
nofde = pberthaopt.nofde
eigem = None
rho = None
Da0 = None
etotal = 0.0
dipx_ref = 0.0
dipy_ref = 0.0
dipz_ref = 0.0
bertha = berthamod.pybertha(pberthaopt.wrapperso)
if not restart:
try:
os.remove(pberthaopt.restartfname)
except OSError:
pass
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
if stdoutprint:
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
ovapm, eigem, fockm, eigen = bertha.run()
if pberthaopt.dumpfiles:
os.rename(vctfilename, 'unpert_vct.txt')
if (fockm is None) or (eigen is None) or (fockm is None) \
or (eigen is None):
raise Exception("Error in bertha run")
if stdoutprint:
sys.stdout.flush()
print("")
print("Final results ")
for i in range(nocc + nopen):
print("eigenvalue %5d %20.8f" %
(i + 1, eigen[i + nshift] - sfact))
print(" lumo %20.8f" % (eigen[i + nshift + 1]))
erep = bertha.get_erep()
etotal = bertha.get_etotal()
ecoul = bertha.get_eecoul()
exc = bertha.get_eexc()
if stdoutprint:
print("")
print("total electronic energy = %30.15f" % (etotal -
(sfact * nocc)))
print("nuclear repulsion energy = %30.15f" % (erep))
print("total energy = %30.15f" % (etotal + erep -
(sfact * nocc)))
print("coulomb energy = %30.15f" % (ecoul))
print("Exc energy = %30.15f" % (exc))
else:
if stdoutprint:
print("Restart: ")
my_file = Path(pberthaopt.restartfname)
if not my_file.is_file():
raise Exception(pberthaopt.restartfname +
" does not exist restart=on")
alldata = numpy.load(pberthaopt.restartfname)
eigem = alldata["eigem"]
Da0 = alldata["Da0"]
rho = alldata["rho"]
etotalnpa = alldata["etotalnpa"]
etotal = etotalnpa[0]
dipx_ref = etotalnpa[1]
dipy_ref = etotalnpa[2]
dipz_ref = etotalnpa[3]
activefname = pberthaopt.activefile
if not os.path.isfile(activefname):
raise Exception("File ", activefname, " does not exist")
envirofname = pberthaopt.envirofile
if not os.path.isfile(envirofname):
raise Exception("File ", envirofname, " does not exist")
embfactory = pyembmod.pyemb(activefname, envirofname,
'adf') #jobtype='adf' is default de facto
#grid_param =[50,110] # psi4 grid parameters (see Psi4 grid table)
#embfactory.set_options(param=grid_param, \
embfactory.set_options(param=pberthaopt.param, \
gtype=pberthaopt.gtype, basis=pberthaopt.basis)
embfactory.set_enviro_func(pberthaopt.excfuncenv)
embfactory.set_thresh_conv(pberthaopt.thresh_conv)
embfactory.set_grid_filename(pberthaopt.gridfname)
# several paramenters to be specified in input- e.g AUG/ADZP for ADF, aug-cc-pvdz for psi4
if (pberthaopt.debug):
import uuid
filename = "adfout_" + str(uuid.uuid4()) + ".txt"
embfactory.set_adf_filenameout(filename)
filename = "psi4out_" + str(uuid.uuid4()) + ".txt"
embfactory.set_psi4_filenameout(filename)
if stdoutprint:
print("embfactory Options:")
print(embfactory.get_options())
embfactory.initialize()
grid = embfactory.get_grid()
if (pberthaopt.debug):
numpy.savetxt("grid.txt", grid)
if not restart:
rho = bertha.get_density_on_grid(grid)
if stdoutprint:
print("Grid dimensions : ", grid.shape)
print(" Rho dimensions : ", rho.shape)
density = numpy.zeros((rho.shape[0], 10))
density[:, 0] = rho
fpot = None
pot = embfactory.get_potential(density)
if (pberthaopt.debug):
numpy.savetxt("initialpot.txt", pot)
#DEBUG
#pot=numpy.zeros(rho.shape[0])
if static_field:
fpot = grid[:, fdir] * fmax
fpot = numpy.ascontiguousarray(fpot, dtype=numpy.double)
if (pberthaopt.debug):
numpy.savetxt("initialfpot.txt", fpot)
if not restart:
if stdoutprint:
#print("TEST density on grid")
#print("Type density", type(density), density.shape)
print("Scalar product", "density.weigt",
numpy.dot(density[:, 0], grid[:, 3]))
print("Dip x", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 0]))
print("Dip y", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 1]))
print("Dip z", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 2]))
bertha.realtime_init()
normalise = 1
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da0 = numpy.matmul(occeigv, numpy.conjugate(occeigv.transpose()))
if stdoutprint:
print("Dump ground state unperturbed density " +
pberthaopt.densityzero)
if pberthaopt.densityzero != "":
bertha.density_to_cube(Da0.T, pberthaopt.densityzero, \
drx=pberthaopt.drx, dry=pberthaopt.dry, drz=pberthaopt.drz, \
margin=pberthaopt.margin)
dipx_ref = numpy.trace(numpy.matmul(Da0, dipx_mat)).real
dipy_ref = numpy.trace(numpy.matmul(Da0, dipy_mat)).real
dipz_ref = numpy.trace(numpy.matmul(Da0, dipz_mat)).real
bertha.finalize()
etotalnpa = numpy.zeros((4))
etotalnpa[0] = etotal
etotalnpa[1] = dipx_ref
etotalnpa[2] = dipy_ref
etotalnpa[3] = dipz_ref
numpy.savez(pberthaopt.restartfname, eigem=eigem, \
Da0=Da0, rho=rho, etotalnpa=etotalnpa)
if stdoutprint:
print("unperturbed Dip x ", dipx_ref)
print("unperturbed Dip y ", dipy_ref)
print("unperturbed Dip z ", dipz_ref)
#if lin_emb=True, a single scf is performed at constant Vemb
maxiter = 20
Dold = Da0
Da = Da0
Eold = etotal
lin_emb = pberthaopt.linemb
dipx_val = 0.0
dipy_val = 0.0
dipz_val = 0.0
dipx_mat = None
dipy_mat = None
dipz_mat = None
for out_iter in range(maxiter):
time_iter_start = time.time()
process_time_iter_start = time.process_time()
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
# run with Vemb included
if static_field:
totpot = pot + fpot
if nofde:
totpot = fpot
totpot = numpy.ascontiguousarray(totpot, dtype=numpy.double)
if (pberthaopt.debug):
numpy.savetxt("fullpot%d.txt" % (out_iter), totpot)
bertha.set_embpot_on_grid(grid, totpot)
else:
if (pberthaopt.debug):
numpy.savetxt("fullpot%d.txt" % (out_iter), pot)
if nofde:
pot = numpy.zeros_like(pot)
bertha.set_embpot_on_grid(grid, pot)
ovapm, eigem, fockm, eigen = bertha.run(eigem)
etotal2 = bertha.get_etotal()
# save the extern pot used in the scf run
# pot_in = pot
# the avg associated to pot
emb_avg_in = numpy.dot(density[:, 0] * grid[:, 3], pot)
#print
if stdoutprint:
print("")
print(
"total electronic energy = %30.15f ... outer iteration :%i" %
((etotal2 - (sfact * nocc)), (out_iter + 1)))
print(
"mean value of embed pot = %30.15f ... outer iteration :%i" %
((emb_avg_in), (out_iter + 1)))
erep = bertha.get_erep()
etotal = bertha.get_etotal()
ecoul = bertha.get_eecoul()
exc = bertha.get_eexc()
if stdoutprint:
print("outer iteration : ", out_iter + 1)
print("total electronic energy = %30.15f" % (etotal -
(sfact * nocc)))
print("nuclear repulsion energy = %30.15f" % (erep))
print("total energy = %30.15f" % (etotal + erep -
(sfact * nocc)))
print("coulomb energy = %30.15f" % (ecoul))
print("Exc energy = %30.15f" % (exc))
if lin_emb:
#rho = bertha.get_density_on_grid(grid)
#density=numpy.zeros((rho.shape[0],10))
#density[:,0] = rho
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da = numpy.matmul(occeigv, numpy.conjugate(occeigv.transpose()))
if stdoutprint:
print("Dump ground state perturbed density " +
pberthaopt.density)
if pberthaopt.density != "":
bertha.density_to_cube(Da.T, pberthaopt.density, drx=pberthaopt.drx, \
dry=pberthaopt.dry, drz=pberthaopt.drz, margin=pberthaopt.margin)
bertha.realtime_init()
normalise = 1
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
numofatom = bertha.get_natoms()
tmpcoords = []
tmpz = []
for i in range(numofatom):
tmpcoords.append(list(bertha.get_coords(i))[0:3])
tmpz.append(list(bertha.get_coords(i))[3])
matcoords = numpy.array(tmpcoords)
vecZ = numpy.array(tmpz)
vec_nuc_dip = numpy.matmul(vecZ.T, matcoords)
nucdipx = vec_nuc_dip[0]
nucdipy = vec_nuc_dip[1]
nucdipz = vec_nuc_dip[2]
bertha.finalize()
break
#if out_iter == (maxiter - 1):
# bertha.finalize()
# raise Exception("Maximum number of SCF cycles reached.\n")
# calculate the embedding potential corresponding to the new density
time_get_density_on_grid_start = time.time()
process_time_get_density_on_grid_start = time.process_time()
rho = bertha.get_density_on_grid(grid)
time_get_density_on_grid_end = time.time()
process_time_get_density_on_grid_end = time.process_time()
print("Fitted density on grid time: %15.5f"%(time_get_density_on_grid_end - time_get_density_on_grid_start), \
" (CPU time: %15.5f"%(process_time_get_density_on_grid_end - process_time_get_density_on_grid_start), ") s ")
density = numpy.zeros((rho.shape[0], 10))
density[:, 0] = rho
pot_old = pot
time_start = time.time()
process_time_start = time.process_time()
pot = embfactory.get_potential(density)
time_end = time.time()
process_time_end = time.process_time()
print("Vemb pot on grid: embfactory.get_potential: %15.5f"%(time_end - time_start), \
" (CPU time: %15.5f"%(process_time_end - process_time_start), ") s ")
#DEBUG
#pot=numpy.zeros_like(rho)
# the avg associated to new embed pot
emb_avg = numpy.dot(density[:, 0] * grid[:, 3], pot)
# form the density matrix
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
iocc = 0
#debug
if stdoutprint:
print("ndim : %i\n" % ndim)
print("nshift : %i\n" % nshift)
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da = numpy.matmul(occeigv, numpy.conjugate(occeigv.transpose()))
diffD = Da - Dold
diffE = etotal2 - Eold
norm_pot = numpy.sqrt(numpy.sum((pot - pot_old)**2))
norm_D = numpy.linalg.norm(diffD, 'fro')
if stdoutprint:
print("2-norm of diffD = ", norm_D,
" ... outer iteration :%i" % (out_iter + 1))
print("E(actual)-E(prev)= ", diffE,
" ... outer iteration :%i" % (out_iter + 1))
print("DE_emb(actual-prev) = %30.15f ... outer iteration :%i" %
((emb_avg_in - emb_avg), (out_iter + 1)))
print("norm_pot(actual-prev) = %30.15f ... outer iteration :%i" %
((norm_pot), (out_iter + 1)))
if (norm_D < (1.0e-6) and norm_pot < (1.0e-4)):
#not needed?
#iocc = 0
#for i in range(ndim):
# if i >= nshift and iocc < nocc:
# for j in range(ndim):
# occeigv[j, iocc] = eigem[j, i]
# iocc = iocc + 1
#Da = numpy.matmul(occeigv,numpy.conjugate(occeigv.transpose()))
if stdoutprint:
print("Dump ground state perturbed density density.cube")
bertha.realtime_init()
dipx_mat, dipy_mat, dipz_mat = bertha.get_realtime_dipolematrix(
0, normalise)
if pberthaopt.density != "":
bertha.density_to_cube(Da.T, pberthaopt.density, drx=pberthaopt.drx, \
dry=pberthaopt.dry, drz=pberthaopt.drz, margin=pberthaopt.margin)
bertha.finalize()
break
time_iter_end = time.time()
process_time_iter_end = time.process_time()
print(" Time for each extrenal iteration: %15.5f"%(time_iter_end - time_iter_start), \
" (CPU time: %15.5f"%(process_time_iter_end - process_time_iter_start), ") s ")
if out_iter == maxiter - 1:
if pberthaopt.density != "":
bertha.density_to_cube(Da.T, pberthaopt.density, drx=pberthaopt.drx, \
dry=pberthaopt.dry, drz=pberthaopt.drz, margin=pberthaopt.margin)
Dold = Da
Eold = etotal2
bertha.realtime_init()
normalise = 1
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
"""
Calculation of the Nuclear dipole (a.u)
"""
##### print("Compute nuclear dipole (a.u.)")
numofatom = bertha.get_natoms()
tmpcoords = []
tmpz = []
for i in range(numofatom):
tmpcoords.append(list(bertha.get_coords(i))[0:3])
tmpz.append(list(bertha.get_coords(i))[3])
matcoords = numpy.array(tmpcoords)
vecZ = numpy.array(tmpz)
vec_nuc_dip = numpy.matmul(vecZ.T, matcoords)
nucdipx = vec_nuc_dip[0]
nucdipy = vec_nuc_dip[1]
nucdipz = vec_nuc_dip[2]
bertha.finalize()
dipx_val = numpy.trace(numpy.matmul(Da, dipx_mat)).real
dipy_val = numpy.trace(numpy.matmul(Da, dipy_mat)).real
dipz_val = numpy.trace(numpy.matmul(Da, dipz_mat)).real
if stdoutprint:
print("")
print("Dip x ", dipx_val)
print("Dip y ", dipy_val)
print("Dip z ", dipz_val)
print("MOLECULAR PROPERTIES of ACTIVE SYSTEM IN EMBEDDING:...")
print(" ")
print("Dipole Moment: ")
print(
"Axis electronic dipole (a.u.) nuclear dipole (a.u.) Total dipole (a.u.) Total dipole (Debye) "
)
print(" x %20.10f %20.10f %20.10f %20.10f " %
(dipx_val, nucdipx, dipx_val + nucdipx,
(dipx_val + nucdipx) * 2.541580))
print(" y %20.10f %20.10f %20.10f %20.10f " %
(dipy_val, nucdipy, dipy_val + nucdipy,
(dipy_val + nucdipy) * 2.541580))
print(" z %20.10f %20.10f %20.10f %20.10f " %
(dipz_val, nucdipz, dipz_val + nucdipz,
(dipz_val + nucdipz) * 2.541580))
print(" ")
tot_dip_vec = numpy.array(
[dipx_val + nucdipx, dipy_val + nucdipy, dipz_val + nucdipz])
print("Molecular dipole module: %20.10f (a.u.) %20.10f (Debye) " %
(numpy.linalg.norm(tot_dip_vec),
numpy.linalg.norm(tot_dip_vec) * 2.541580))
print(
"MOLECULAR PROPERTIES of ACTIVE SYSTEM WITHOUT EMBEDDING (free active system):..."
)
print(" ")
print("Dipole Moment: ")
print(
"Axis electronic dipole (a.u.) nuclear dipole (a.u.) Total dipole (a.u.) Total dipole (Debye) "
)
print(" x %20.10f %20.10f %20.10f %20.10f " %
(dipx_ref, nucdipx, dipx_ref + nucdipx,
(dipx_ref + nucdipx) * 2.541580))
print(" y %20.10f %20.10f %20.10f %20.10f " %
(dipy_ref, nucdipy, dipy_ref + nucdipy,
(dipy_ref + nucdipy) * 2.541580))
print(" z %20.10f %20.10f %20.10f %20.10f " %
(dipz_ref, nucdipz, dipz_ref + nucdipz,
(dipz_ref + nucdipz) * 2.541580))
print(" ")
tot_dip_vec = numpy.array(
[dipx_ref + nucdipx, dipy_ref + nucdipy, dipz_ref + nucdipz])
print("Molecular dipole module: %20.10f (a.u.) %20.10f (Debye) " %
(numpy.linalg.norm(tot_dip_vec),
numpy.linalg.norm(tot_dip_vec) * 2.541580))
if stdoutprint:
print("Dipole moment analitical: Tr(D dip_mat)")
print("dipX_mat dim: %i,%i\n" % (dipx_mat.shape))
print("dipY_mat dim: %i,%i\n" % (dipy_mat.shape))
print("dipZ_mat dim: %i,%i\n" % (dipz_mat.shape))
print("Da dim: %i,%i\n" % (Da.shape))
print("TEST dipole moment from density on grid numerical integration")
print(" ")
#print("Type density", type(density), density.shape)
print("Scalar product", "density.weigt",
numpy.dot(density[:, 0], grid[:, 3]))
print("Dip x", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 0]))
print("Dip y", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 1]))
print("Dip z", "density.weigt",
-1. * numpy.dot(density[:, 0] * grid[:, 3], grid[:, 2]))
print(" ")
sys.stdout.flush()
print("Final results of SplitSCF")
for i in range(nocc + nopen):
print("eigenvalue %5d %20.8f" % (i + 1, eigen[i + nshift] - sfact))
print(" lumo %20.8f" % (eigen[i + nshift + 1]))
return ovapm, eigem, fockm, eigen, pot
import ctypes
import numpy
import sys
import re
import os.path
from numpy.linalg import eigvalsh
from scipy.linalg import eigh
sys.path.insert(0, '../src/')
import berthamod
bertha = berthamod.pybertha("../../lib/bertha_wrapper.so")
fittcoefffname = "fitcoeff.txt"
vctfilename = "vct.txt"
ovapfilename = "ovap.txt"
fnameinput = "input.inp"
fittfname = "fitt2.inp"
verbosity = -1
dumpfiles = 1
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_verbosity(verbosity)
def normal_run(pberthaopt, args):
import pyembmod
print("Options: ")
print(args)
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
print("SO File ", pberthaopt.wrapperso, " does not exist")
return False
ovapm, eigem, fockm, eigen, pot = pyberthaembed.runspberthaembed(
pberthaopt, restart=False, stdoutprint=True)
print("CHECK")
print("eigem dim: %i,%i\n" % (eigem.shape[0], eigem.shape[1]))
if ovapm is None:
return False
# emfactory -> embedding potential corresponding to Da
activefname = pberthaopt.activefile
if not os.path.isfile(activefname):
raise Exception("File ", activefname, " does not exist")
envirofname = pberthaopt.envirofile
if not os.path.isfile(envirofname):
raise Exception("File ", envirofname, " does not exist")
embfactory = pyembmod.pyemb(activefname, envirofname,
'adf') #jobtype='adf' is default de facto
#grid_param =[50,110] # psi4 grid parameters (see Psi4 grid table)
#embfactory.set_options(param=grid_param, \
embfactory.set_options(param=pberthaopt.param, \
gtype=pberthaopt.gtype, basis=pberthaopt.basis)
embfactory.set_enviro_func(pberthaopt.excfuncenv)
# several paramenters to be specified in input- e.g AUG/ADZP for ADF, aug-cc-pvdz for psi4
embfactory.initialize()
grid = embfactory.get_grid()
bertha = berthamod.pybertha(pberthaopt.wrapperso)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
# just an additional restart, so we can call bertha.realtime_init()
bertha.set_embpot_on_grid(grid, pot)
#the newly converged eigem and rho
ovapm, eigem, fockm, eigen = bertha.run(eigem)
rho = bertha.get_density_on_grid(grid)
density = numpy.zeros((rho.shape[0], 10))
density[:, 0] = rho
# the embedding potential from converged density
pot = embfactory.get_potential(density)
bertha.set_embpot_on_grid(grid, pot)
bertha.realtime_init()
print("Start RT")
debug = args.debug
dt = args.dt
t_int = args.totaltime
niter = int(t_int / dt)
print("Debug: ", debug)
print("dt : ", dt)
print("ndim : ", ndim)
print("nocc : ", nocc)
print("Total time : ", t_int)
print("Number of iterations: ", niter)
sys.stdout.flush()
ene_list = []
dip_list = []
weight_list = []
imp_list = []
Enuc_list = []
C = eigem
D_0 = numpy.zeros((ndim, ndim), dtype=numpy.complex128)
for num in range(nocc):
D_0[num + nshift, num + nshift] = 1.0 + 0.0j
fo = sys.stderr
if debug:
fo = open("debug_info.txt", "w")
#print type(eigem)
#C_inv used to backtransform D(AO)
try:
C_inv = numpy.linalg.inv(eigem)
except LinAlgError:
print("Error in numpy.linalg.inv of eigem")
return False
if debug:
test = numpy.matmul(C_inv, eigem)
fo.write("Check if atol is 1.e-14 for inversion of C: %s\n"% \
numpy.allclose(numpy.eye((ndim),dtype=numpy.complex128), \
test,atol=1.e-14))
if debug:
diff = test - numpy.eye((ndim), dtype=numpy.complex128)
mdiff = numpy.max(diff)
fo.write(" maxdiff is: %.12e %.12e\n" % (mdiff.real, mdiff.imag))
if debug:
test = numpy.matmul(numpy.conjugate(C.T), numpy.matmul(ovapm, C))
fo.write("Check orthonormal orbitals (atol = 1.e-14): %s\n"% \
numpy.allclose(numpy.eye((ndim),dtype=numpy.complex128), \
test, atol=1.e-14))
diff = test - numpy.eye((ndim), dtype=numpy.complex128)
mdiff = numpy.max(diff)
fo.write(" maxdiff is: %.12e %.12e\n" % (mdiff.real, mdiff.imag))
#build density in ao basis
occeigv = numpy.zeros((ndim, nocc), dtype=numpy.complex128)
iocc = 0
for i in range(ndim):
if i >= nshift and iocc < nocc:
for j in range(ndim):
occeigv[j, iocc] = eigem[j, i]
iocc = iocc + 1
Da = numpy.matmul(occeigv, numpy.conjugate(occeigv.transpose()))
print("")
print("Dump ground state density density0.cube")
bertha.density_to_cube(Da.T, "density0.cube", margin=5.0)
print("Done")
if debug:
#check trace(S Da)
trace_ds = numpy.trace(numpy.matmul(Da, ovapm))
trace_dsfock = numpy.trace(numpy.matmul(Da, fockm))
fo.write("Density matrix trace at t0: %.12e %.12e \n" %
(trace_ds.real, trace_ds.imag))
fo.write("Trace of fock*density at t0: %.12e %.12e \n" %
(trace_dsfock.real, trace_dsfock.imag))
normalise = 1
dip_mat = None
dipx_mat, dipy_mat, dipz_mat = \
bertha.get_realtime_dipolematrix (0, normalise)
if (args.direction == 4):
dip_mat = dipx_mat
elif (args.direction == 3):
dip_mat = dipy_mat
elif (args.direction == 2):
dip_mat = dipz_mat
if debug:
fockmh = numpy.conjugate(fockm.T)
diff_fockmh = fockm - fockmh
mdiff = numpy.max(diff_fockmh)
fo.write("Check max diff fockm-fockmh: %.12e %.12e\n"%\
(mdiff.real, mdiff.imag))
fo.write("Fockm (t=0) is hermitian: %s \n" %
numpy.allclose(fockm, fockmh, atol=1.e-15))
molist = args.select.split("&")
occlist = molist[0].split(";")
occlist = [int(m) for m in occlist]
virtlist = molist[1].split(";")
virtlist = [int(m) for m in virtlist]
if (args.pulse == "analytic"):
Amp = args.pulseFmax
# to check
dipz_mo = numpy.matmul(numpy.conjugate(C.T), numpy.matmul(dip_mat, C))
if args.select_pert:
dipz_mo = rtutil.dipole_selection(dipz_mo, nshift, nocc, occlist,
virtlist, fo, debug)
print(" Perturb with analytic kick ")
u0 = rtutil.exp_opmat(dipz_mo, numpy.float_(-Amp), debug, fo)
Dp_init = numpy.matmul(u0, numpy.matmul(D_0, numpy.conjugate(u0.T)))
#transform back Dp_int
Da = numpy.matmul(C, numpy.matmul(Dp_init, numpy.conjugate(C.T)))
D_0 = Dp_init
print("Start first mo_fock_mid_forwd_eval ")
print("CHECK")
print("C dim : %i,%i\n" % (C.shape[0], C.shape[1]))
print("C^-1 dim : %i,%i\n" % (C_inv.shape[0], C_inv.shape[1]))
fock_mid_init = rtutil.mo_fock_mid_forwd_eval(bertha,Da,fockm,0,numpy.float_(dt),\
dip_mat,C,C_inv,ovapm,ndim, debug, fo, args.pulse, args.pulseFmax, args.pulsew, args.t0, args.pulseS,
args.propthresh)
if (fock_mid_init is None):
print("Error accurs in mo_fock_mid_forwd_eval")
return False
if debug:
fock_mid_h = numpy.conjugate(fock_mid_init.T)
diff_fock_mid_h = fock_mid_init - fock_mid_h
fo.write("Max diff fock_mid_init-fock_mid_h" %
(numpy.max(diff_fock_mid_h)))
fo.write('Fockm (t=1/2) is hermitian: %s\n' %
numpy.allclose(fock_mid_init, fock_mid_h, atol=1.e-14))
fockp_mid_init = numpy.matmul(numpy.conjugate(C.T),
numpy.matmul(fock_mid_init, C))
u = rtutil.exp_opmat(fockp_mid_init, numpy.float_(dt), debug, fo)
#u=rtutil.exp_opmat(fockp_mid_init,numpy.float_(dt),debug,fo)
#u=scila.expm(-1.j*fockp_mid_init*dt)
temp = numpy.matmul(D_0, numpy.conjugate(u.T))
Dp_t1 = numpy.matmul(u, temp)
#check u if unitary
if debug:
test_u = numpy.matmul(u, numpy.conjugate(u.T))
fo.write('U is unitary : %s' %
numpy.allclose(test_u, numpy.eye(u.shape[0]), atol=1.e-14))
#backtrasform Dp_t1
D_t1 = numpy.matmul(C, numpy.matmul(Dp_t1, numpy.conjugate(C.T)))
if debug:
diff = D_t1 - Da
mdiff = numpy.max(diff)
fo.write("Max diff density: %.12e %.12e \n" % (mdiff.real, mdiff.imag))
dip_list.append(numpy.trace(numpy.matmul(Da, dip_mat)))
dip_list.append(numpy.trace(numpy.matmul(D_t1, dip_mat)))
if (args.pulse == "analytic"):
if (occlist[0] != -2):
#dipoleanalysis
res = rtutil.dipoleanalysis(dipz_mo, D_0, occlist, virtlist,
nshift, fo, debug)
weight_list.append(res)
res = rtutil.dipoleanalysis(dipz_mo, Dp_t1, occlist, virtlist,
nshift, fo, debug)
weight_list.append(res)
if debug:
fo.write("Dipole: %.12e\n" %
(numpy.trace(numpy.matmul(Da, dip_mat))).real)
fo.write("Dipole: %.12e\n" %
(numpy.trace(numpy.matmul(D_t1, dip_mat))).real)
if debug:
tfock = numpy.trace(numpy.matmul(D_t1, fockm))
fo.write("Trace fock*density t1: %.12e, %.12e\n" %
(tfock.real, tfock.imag))
trace_ds = numpy.trace(numpy.matmul(D_t1, ovapm))
fo.write(" Traceds: %.12e %.12ei\n" % (trace_ds.real, trace_ds.imag))
Ndip_z = 0.0
#estrarre le 3 componenti del dipolo nucleare
D_ti = D_t1
Dp_ti = Dp_t1
#aggiungere repulsione nucleare
#Enuc_list.append(-func_t0*Ndip_z+Nuc_rep) #just in case of non-zero nuclear dipole
start = time.time()
cstart = time.process_time()
fockm_ti = bertha.get_realtime_fock(D_ti.T)
end = time.time()
cend = time.process_time()
print("RealTime Fock Time: %15.5f" % (end - start),
" (CPU: %15.5f" % (cend - cstart), " ) s")
print("RealTime Fock Time Without Py: %15.5f"%(bertha.get_focktime()), \
" (CPU: %15.5f"%(bertha.get_fockctime()), " ) s")
print("")
ene_list.append(numpy.trace(numpy.matmul(Da, fockm)))
ene_list.append(numpy.trace(numpy.matmul(D_ti, fockm_ti)))
print("Starting iterations ...")
print("")
fock_mid_backwd = numpy.copy(fock_mid_init)
return run_iterations_from_to (1, niter, bertha, embfactory, args, fock_mid_backwd, \
dt, dip_mat, C, C_inv, ovapm, ndim, debug, Dp_ti, dip_list, ene_list, \
weight_list, fo, D_ti, occlist)
def runspberthaembedrt(pberthaopt):
sys.path.insert(0, pberthaopt.berthamodpath)
import berthamod
print("Options: ")
for att in [a for a in dir(pberthaopt) if not a.startswith('__')]:
print(att, " = ", getattr(pberthaopt, att))
print("")
print("")
print("")
if not os.path.isfile(pberthaopt.wrapperso):
print("SO File ", pberthaopt.wrapperso, " does not exist")
exit(1)
bertha = berthamod.pybertha(pberthaopt.wrapperso)
fittcoefffname = pberthaopt.fitcoefffile
vctfilename = pberthaopt.vctfile
ovapfilename = pberthaopt.ovapfile
fnameinput = pberthaopt.inputfile
if not os.path.isfile(fnameinput):
print("File ", fnameinput, " does not exist")
exit(1)
fittfname = pberthaopt.fittfile
if not os.path.isfile(fittfname):
print("File ", fittfname, " does not exist")
exit(1)
verbosity = pberthaopt.verbosity
dumpfiles = int(pberthaopt.dumpfiles)
bertha.set_fittcoefffname(fittcoefffname)
bertha.set_ovapfilename(ovapfilename)
bertha.set_vctfilename(vctfilename)
bertha.set_fnameinput(fnameinput)
bertha.set_fittfname(fittfname)
bertha.set_thresh(pberthaopt.thresh)
bertha.set_verbosity(verbosity)
bertha.set_dumpfiles(dumpfiles)
bertha.set_densitydiff(1)
bertha.init()
ndim = bertha.get_ndim()
nshift = bertha.get_nshift()
nocc = bertha.get_nocc()
sfact = bertha.get_sfact()
nopen = bertha.get_nopen()
print("Verbosity : ", verbosity)
print("Dumpfiles : ", dumpfiles)
print("")
print("Matrix dimension: ", ndim)
print(" nocc: ", nocc)
print(" nshift: ", nshift)
print(" nopen: ", nopen)
print(" level shift: ", sfact)
print("")
#generate a sample grid
npoints = 10
grid = numpy.zeros((npoints, 4))
grid = numpy.ascontiguousarray(grid, dtype=numpy.double)
pot = numpy.zeros(npoints)
pot = numpy.ascontiguousarray(pot, dtype=numpy.double)
x = -1.0
y = -100.0
z = -1000.0
w = 1.0
for i in range(npoints):
grid[i, 0] = x
grid[i, 1] = y
grid[i, 2] = z
grid[i, 3] = w
x += 1.0
y += 1.0
z += 1.0
w += 0.1
start = time.time()
cstart = time.process_time()
bertha.set_embpot_on_grid(grid, pot)
#main run here
ovapm, eigem, fockm, eigen = bertha.run()
density = bertha.get_density_on_grid(grid)
for i in range(npoints):
val = grid[i, 0] * grid[i, 1] * grid[i, 2] * grid[i, 3]
print("Python L: %15.5f vs %15.5f" % (density[i], val))
end = time.time()
cend = time.process_time()
print("Totaltime: ", end - start, " (CPU time: ", cend - cstart, ") s ")
print("MainRun Time: ", bertha.get_mainruntime() , \
" (CPU time: " , bertha.get_mainrunctime(), ") s ")
sys.stdout.flush()