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qmcchem
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cluster: Jast opt for SCF WV

This commit is contained in:
Abdallah Ammar 2021-04-27 04:04:40 +02:00
parent e9962280dc ba1c326616
commit a93803151e
22 changed files with 3145 additions and 170 deletions
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181
bin/jast_opt.py
View File

@ -8,10 +8,13 @@ import os
import time
import subprocess
from math import sqrt
#
#from bayes_opt import BayesianOptimization
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
# this should give: /home/ammar/qmcchem
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# this should add: /home/ammar/qmcchem/EZFIO/Python/
from ezfio import ezfio
@ -22,7 +25,7 @@ block_time = 20
def main():
if len(sys.argv) != 2:
print("Usage: %s <EZFIO_DIRECTORY>"%sys.argv[0])
sys.exti(1)
sys.exit(1)
filename = sys.argv[1]
ezfio.set_file(filename)
@ -47,7 +50,7 @@ def main():
def get_params_pen():
d = ezfio.jastrow_jast_pen
return np.array([d[m[0]] for m in atom_map])
return np.array( [d[m[0]] for m in atom_map])
def get_energy():
@ -60,6 +63,21 @@ def main():
else:
return None, None
#####################################################################################################
def get_energy_deriv_nucPar():
# !!!
buffer = subprocess.check_output(['qmcchem', 'result', filename], encoding='UTF-8')
# !!!
if buffer.strip()!= "":
e_der1 = [ buffer.splitlines()[13].split()[2], buffer.splitlines()[14].split()[2], buffer.splitlines()[15].split()[2] ]
err_der1 = [ buffer.splitlines()[13].split()[4], buffer.splitlines()[14].split()[4], buffer.splitlines()[15].split()[4] ]
e_der2 = [ buffer.splitlines()[2].split()[2], buffer.splitlines()[3].split()[2], buffer.splitlines()[4].split()[2] ]
err_der2 = [ buffer.splitlines()[2].split()[4], buffer.splitlines()[3].split()[4], buffer.splitlines()[4].split()[4] ]
return e_der1, e_der2
else:
return None
#####################################################################################################
def get_variance():
buffer = subprocess.check_output(['qmcchem', 'result', '-e',
'e_loc_qmcvar', filename],
@ -99,67 +117,110 @@ def main():
# '-w', '10',
# filename])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
'-l', str(block_time),
filename])
'-l', str(block_time), filename])
# !!!
# !!!
#####################################################################################################
# Only for CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr.
# !!!
def fprime(x):
# !!!
print ("derivative on: x = %s"%str(x))
# !!!
e_der1, e_der2 = get_energy_deriv_nucPar()
e, _ = get_energy()
energy_deriv_0 = 2. * ( float(e_der1[0]) - e * float(e_der2[0]) )
energy_deriv_1 = 2. * ( float(e_der1[1]) - e * float(e_der2[1]) )
energy_deriv = np.array([ energy_deriv_0 , energy_deriv_1 ])
# !!!
print(energy_deriv)
# !!!
return energy_deriv
# !!!
#####################################################################################################
# !!!
memo_energy = {'fmin': 100000000.}
def f(x):
print ("x = %s"%str(x))
h = str(x)
if h in memo_energy:
return memo_energy[h]
set_params_pen(x)
set_vmc_params()
pid = os.fork()
if pid == 0:
run_qmc()
os._exit(os.EX_OK)
else:
import atexit
atexit.register(stop_qmc)
err = thresh+1.
time.sleep(3.*block_time/4.)
local_thresh = thresh
while err > local_thresh:
time.sleep(block_time)
e, e_err = get_energy()
variance, v_err = get_variance()
if e is None or variance is None:
continue
energy = e + variance
err = sqrt(e_err*e_err+v_err*v_err)
print(" %f %f %f %f %f %f"%(e, e_err, variance, v_err, energy, err))
if (energy-2.*err) > memo_energy['fmin']+thresh:
local_thresh = 10.*thresh
elif (energy+2.*err) < memo_energy['fmin']-thresh:
local_thresh = 10.*thresh
# Check if PID is still running
try:
os.kill(pid,0)
except OSError:
print("---")
break
stop_qmc()
os.wait()
memo_energy[h] = energy + err
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
return energy
print ("x = %s"%str(x))
# !!!
h = str(x)
if h in memo_energy:
return memo_energy[h]
# !!!
set_params_pen(x)
set_vmc_params()
# !!!
pid = os.fork()
if pid == 0:
# In child process
run_qmc()
# Exit with status os.EX_OK using os._exit() method. The value of os.EX_OK is 0
os._exit(os.EX_OK)
else:
# In parent process
import atexit
atexit.register(stop_qmc)
# !!!
time.sleep(3.*block_time/4.)
# !!!
err = thresh+1.
local_thresh = thresh
while err > local_thresh:
time.sleep(block_time)
e, e_err = get_energy()
variance, v_err = get_variance()
if e is None or variance is None:
continue
# !!!
#energy = e + variance
#err = sqrt(e_err*e_err+v_err*v_err)
energy = e
err = e_err
# !!!
#print(" %f %f %f %f %f %f"%(e, e_err, variance, v_err, energy, err))
# !!!
print(" %f %f"%(energy, err))
if (energy-2.*err) > memo_energy['fmin']+thresh:
local_thresh = 10.*thresh
elif (energy+2.*err) < memo_energy['fmin']-thresh:
local_thresh = 10.*thresh
# !!!
# Check if PID is still running
try:
os.kill(pid,0)
except OSError:
print("---")
break
stop_qmc()
os.wait()
# !!!
#memo_energy[h] = energy + err
memo_energy[h] = energy
# !!!
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
return energy
# !!!
def run():
x = get_params_pen()
if sum(x) == 0.:
jast_a_up_dn = ezfio.jastrow_jast_a_up_dn
x += jast_a_up_dn
opt = sp.optimize.minimize(f,x,method="Powell",
options= {'disp':True, 'ftol':thresh,'xtol':0.02})
print("x = "+str(opt))
set_params_pen(opt['x'])
x = get_params_pen()
# !!!
if sum(x) == 0.:
jast_a_up_dn = ezfio.jastrow_jast_a_up_dn
x += jast_a_up_dn
# !!!
opt = sp.optimize.minimize(f,x,method="Powell", options= {'disp':True, 'ftol':thresh,'xtol':0.02})
# !!!
bnds = ((0.001, 100), (0.001, 100))
#opt = sp.optimize.minimize(f, x, method='CG', jac=fprime, options={'gtol': thresh, 'disp': True})
#opt = sp.optimize.minimize(f, x, method='TNC', jac=fprime, options={'gtol': thresh, 'disp': True}, bounds=bnds)
#opt = sp.optimize.minimize(f, x, method='Newton-CG', jac=fprime)
#opt = sp.optimize.minimize(f, x, method='trust-constr', jac=fprime)
print("x = "+str(opt))
set_params_pen(opt['x'])
# !!!
# !!!
run()
# !!!
# !!!
if __name__ == '__main__':
main()

39
src/JASTROW/jastrow_simple.irp.f
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@ -4,7 +4,7 @@
BEGIN_PROVIDER [ double precision , jast_elec_Simple_value, (elec_num_8) ]
implicit none
BEGIN_DOC
! J(i) = \sum_j a.rij/(1+b^2.rij) - \sum_A (a.riA/(1+a.riA))^2
! J(i) = \sum_j a.rij/(1+b.rij) - \sum_A (a.riA/(1+a.riA))^2
END_DOC
integer :: i,j
double precision :: a, b, rij, tmp
@ -20,10 +20,11 @@ implicit none
enddo
enddo
a = 0.5*jast_a_up_up
a = 0.5d0*jast_a_up_up
b = jast_b_up_up
do j=1,elec_alpha_num
! parallele spin up-up
do j=1,elec_alpha_num-1
!DIR$ LOOP COUNT (50)
do i=j+1,elec_alpha_num
rij = elec_dist(i,j)
@ -33,7 +34,8 @@ implicit none
enddo
enddo
do j=elec_alpha_num+1,elec_num
! parallele spin dn-dn
do j=elec_alpha_num+1,elec_num-1
!DIR$ LOOP COUNT (50)
do i=j+1,elec_num
rij = elec_dist(i,j)
@ -43,9 +45,11 @@ implicit none
enddo
enddo
a = 0.5*jast_a_up_dn
a = 0.5d0*jast_a_up_dn
b = jast_b_up_dn
! anti-parallele spin
do j=1,elec_alpha_num
!DIR$ LOOP COUNT (50)
do i=elec_alpha_num+1,elec_num
@ -190,6 +194,31 @@ BEGIN_PROVIDER [ double precision , jast_elec_Simple_lapl, (elec_num_8) ]
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER[ double precision, jast_elec_Simple_deriv_nucPar, (nucl_num) ]
implicit none
BEGIN_DOC
! Variation of the Jastrow factor with respect to nuclear parameters
END_DOC
integer :: i, j
double precision :: a, rij, tmp1, tmp2
do j = 1, nucl_num
a = jast_pen(j)
tmp2 = 0.d0
!DIR$ LOOP COUNT (100)
do i = 1, elec_num
rij = nucl_elec_dist(j,i)
tmp1 = (1.d0+a*rij)*(1.d0+a*rij)*(1.d0+a*rij)
tmp2 += rij*rij/tmp1
end do
jast_elec_Simple_deriv_nucPar(j) = -2.d0 * a * tmp2
end do
END_PROVIDER

3
src/MAIN/qmcchem_info.irp.f
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@ -13,6 +13,9 @@ program qmcchem_info
endif
print *, 'Number of determinants : ', det_num
print *, 'Number of unique alpha/beta determinants : ', det_alpha_num, det_beta_num
if (utilise_svd) then
print *, 'SVD rank : ', n_svd_coefs
endif
print *, 'Closed-shell MOs : ', mo_closed_num
print *, 'Number of MOs in determinants : ', num_present_mos
! print *, 'Det alpha norm:'

51
src/MAIN/test_debug.irp.f Normal file
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@ -0,0 +1,51 @@
program qmcchem_info
implicit none
PROVIDE ezfio_filename
double precision :: cpu0, cpu1
character*(8) :: str_n
integer :: iargc
integer :: imax
if (command_argument_count() > 1) then
call get_command_argument(2,str_n)
read(str_n,*) imax
else
imax = 100
endif
print *, 'Number of determinants : ', det_num
print *, 'Number of unique alpha/beta determinants : ', det_alpha_num, det_beta_num
print *, 'Closed-shell MOs : ', mo_closed_num
print *, 'Number of MOs in determinants : ', num_present_mos
! print *, 'Det alpha norm:'
! print *, det_alpha_norm
! print *, 'Det beta norm:'
! print *, det_beta_norm
call step1
call cpu_time (cpu0)
call step2(imax)
call cpu_time (cpu1)
print *, 'Time for the calculation of E_loc (ms) : ', 1000.*(cpu1-cpu0)/float(imax)
end
subroutine step1
implicit none
print *, 'E_loc : ', E_loc
print *, 'E_loc_svd : ', E_loc_svd
integer :: i
do i=1,elec_num
print *, 'x', psi_grad_psi_inv_x(i), psi_grad_psi_inv_x_SVD(i)
print *, 'y', psi_grad_psi_inv_y(i), psi_grad_psi_inv_y_SVD(i)
print *, 'z', psi_grad_psi_inv_z(i), psi_grad_psi_inv_z_SVD(i)
print *, 'l', psi_lapl_psi_inv(i), psi_lapl_psi_inv_SVD(i)
print *, ''
enddo
end
subroutine step2(imax)
implicit none
integer, intent(in) :: imax
integer :: i
do i=1,imax
PROVIDE E_loc
TOUCH elec_coord
enddo
end

6
src/PROPERTIES/properties_ci.irp.f
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@ -38,7 +38,7 @@ BEGIN_PROVIDER [ double precision, ci_h_psidet, (size_ci_h_psidet) ]
do l=1,elec_alpha_num
T += det_alpha_grad_lapl(4,l,i)*det_beta_value (j)
enddo
do l=elec_beta_num+1,elec_num
do l=elec_alpha_num+1,elec_num
T += det_beta_grad_lapl (4,l,j)*det_alpha_value(i)
enddo
ci_h_psidet(k) = -0.5d0*T + E_pot * det_alpha_value(i)*det_beta_value (j)
@ -98,7 +98,7 @@ BEGIN_PROVIDER [ double precision, ci_h_matrix, (size_ci_h_matrix) ]
do e=1,elec_alpha_num
g += det_alpha_grad_lapl(4,e,m) * det_beta_value (n)
enddo
do e=elec_beta_num+1,elec_num
do e=elec_alpha_num+1,elec_num
g += det_alpha_value(m) * det_beta_grad_lapl(4,e,n)
enddo
T = g
@ -169,7 +169,7 @@ BEGIN_PROVIDER [ double precision, ci_h_matrix_diag, (size_ci_h_matrix_diag) ]
do e=1,elec_alpha_num
g += det_alpha_grad_lapl(4,e,m) * det_beta_value (n)
enddo
do e=elec_beta_num+1,elec_num
do e=elec_alpha_num+1,elec_num
g += det_alpha_value(m) * det_beta_grad_lapl(4,e,n)
enddo
T = g

229
src/PROPERTIES/properties_deriv_jast.irp.f
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@ -9,15 +9,17 @@ BEGIN_PROVIDER [ double precision, E_deriv_nucPar_loc1, (size_E_deriv_nucPar_lo
integer :: i
do i=1,nucl_num
E_deriv_nucPar_loc1(i) = E_loc*jast_elec_Simple_deriv_nucPar(i)
do i = 1, nucl_num
E_deriv_nucPar_loc1(i) = E_loc*jast_elec_Simple_deriv_nucPar(i)
enddo
E_deriv_nucPar_loc1_min = min(E_deriv_nucPar_loc1_min,minval(E_deriv_nucPar_loc1))
E_deriv_nucPar_loc1_max = max(E_deriv_nucPar_loc1_max,maxval(E_deriv_nucPar_loc1))
SOFT_TOUCH E_deriv_nucPar_loc1_min E_deriv_nucPar_loc1_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, E_deriv_nucPar_loc2, (size_E_deriv_nucPar_loc2) ]
implicit none
BEGIN_DOC
@ -29,7 +31,7 @@ BEGIN_PROVIDER [ double precision, E_deriv_nucPar_loc2, (size_E_deriv_nucPar_lo
integer :: i
do i=1,nucl_num
E_deriv_nucPar_loc2(i) = jast_elec_Simple_deriv_nucPar(i)
E_deriv_nucPar_loc2(i) = jast_elec_Simple_deriv_nucPar(i)
enddo
E_deriv_nucPar_loc2_min = min(E_deriv_nucPar_loc2_min,minval(E_deriv_nucPar_loc2))
@ -37,6 +39,38 @@ BEGIN_PROVIDER [ double precision, E_deriv_nucPar_loc2, (size_E_deriv_nucPar_lo
SOFT_TOUCH E_deriv_nucPar_loc2_min E_deriv_nucPar_loc2_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, E_deriv_bPar_loc1 ]
implicit none
BEGIN_DOC
! Local energy variation with respect to parameter b
END_DOC
E_deriv_bPar_loc1 = E_loc*J_deriv_bPar_ex
E_deriv_bPar_loc1_min = min(E_deriv_bPar_loc1_min, E_deriv_bPar_loc1)
E_deriv_bPar_loc1_max = max(E_deriv_bPar_loc1_max, E_deriv_bPar_loc1)
SOFT_TOUCH E_deriv_bPar_loc1_min E_deriv_bPar_loc1_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, E_deriv_bPar_loc2 ]
implicit none
BEGIN_DOC
! Local energy variation with respect to parameter b
END_DOC
E_deriv_bPar_loc2 = J_deriv_bPar_ex
E_deriv_bPar_loc2_min = min(E_deriv_bPar_loc2_min, E_deriv_bPar_loc2)
E_deriv_bPar_loc2_max = max(E_deriv_bPar_loc2_max, E_deriv_bPar_loc2)
SOFT_TOUCH E_deriv_bPar_loc2_min E_deriv_bPar_loc2_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, J_deriv_nucPar_verif, (size_J_deriv_nucPar_verif) ]
implicit none
BEGIN_DOC
@ -45,80 +79,157 @@ BEGIN_PROVIDER [ double precision, J_deriv_nucPar_verif, (size_J_deriv_nucPar_v
! Dimensions : nucl_num
END_DOC
integer :: i,j
double precision :: sqt_eps = 1d-3, der1, der2, pos1, pos2, pos0
integer :: i, j
double precision :: eps = 1d-7, der1, der2, pos0
do j=1,nucl_num
!!
pos0 = sqt_eps * jast_pen(j)
!!
jast_pen(j) = jast_pen(j) + pos0
TOUCH jast_pen
pos1 = jast_pen(j)
!DIR$ LOOP COUNT (100)
do i=1,elec_num
der1 += jast_elec_Simple_value(i)
enddo
!!
jast_pen(j) = jast_pen(j) - 2.d0 * pos0
TOUCH jast_pen
pos2 = jast_pen(j)
!DIR$ LOOP COUNT (100)
do i=1,elec_num
der2 += jast_elec_Simple_value(i)
enddo
!!
J_deriv_nucPar_verif(j) = 0.5d0 * (der1 - der2) / pos0
!!
enddo
do j = 1, nucl_num
!!!
pos0 = eps * jast_pen(j)
!!!
jast_pen(j) = jast_pen(j) + pos0
TOUCH jast_pen
der1 = 0.d0
!DIR$ LOOP COUNT (100)
do i = 1, elec_num
der1 += jast_elec_Simple_value(i)
end do
!!!
jast_pen(j) = jast_pen(j) - 2.d0 * pos0
TOUCH jast_pen
der2 = 0.d0
!DIR$ LOOP COUNT (100)
do i = 1, elec_num
der2 += jast_elec_Simple_value(i)
end do
!!!
J_deriv_nucPar_verif(j) = 0.5d0 * (der1 - der2) / pos0
!!!
end do
J_deriv_nucPar_verif_min = min(J_deriv_nucPar_verif_min,minval(J_deriv_nucPar_verif))
J_deriv_nucPar_verif_max = max(J_deriv_nucPar_verif_max,maxval(J_deriv_nucPar_verif))
SOFT_TOUCH J_deriv_nucPar_verif_min J_deriv_nucPar_verif_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, E_deriv_nucPar_verif, (size_E_deriv_nucPar_verif) ]
BEGIN_PROVIDER [ double precision, J_deriv_nucPar_ex, (size_J_deriv_nucPar_ex) ]
implicit none
BEGIN_DOC
! Local energy variation with respect to nuclear parameters: verification
! Jastrow variation with respect to nuclear parameters
!
! Dimensions : nucl_num
END_DOC
integer :: j
double precision :: sqt_eps = 1d-3, der1, der2, pos1, pos2, pos0
do j=1,nucl_num
!!
pos0 = sqt_eps * jast_pen(j)
!!
jast_pen(j) = jast_pen(j) + pos0
TOUCH jast_pen
pos1 = jast_pen(j)
der1 = E_loc
!!DIR$ LOOP COUNT (100)
!do i=1,elec_num
! der1 += jast_elec_Simple_value(i)
!enddo
!!
jast_pen(j) = jast_pen(j) - 2.d0 * pos0
TOUCH jast_pen
pos2 = jast_pen(j)
der2 = E_loc
!!DIR$ LOOP COUNT (100)
!do i=1,elec_num
! der2 += jast_elec_Simple_value(i)
!enddo
!!
E_deriv_nucPar_verif(j) = 0.5d0 * (der1 - der2) / pos0
!!
enddo
do j = 1, nucl_num
J_deriv_nucPar_ex(j) = jast_elec_Simple_deriv_nucPar(j)
end do
E_deriv_nucPar_verif_min = min(E_deriv_nucPar_verif_min,minval(E_deriv_nucPar_verif))
E_deriv_nucPar_verif_max = max(E_deriv_nucPar_verif_max,maxval(E_deriv_nucPar_verif))
SOFT_TOUCH E_deriv_nucPar_verif_min E_deriv_nucPar_verif_max
J_deriv_nucPar_ex_min = min(J_deriv_nucPar_ex_min,minval(J_deriv_nucPar_ex))
J_deriv_nucPar_ex_max = max(J_deriv_nucPar_ex_max,maxval(J_deriv_nucPar_ex))
SOFT_TOUCH J_deriv_nucPar_ex_min J_deriv_nucPar_ex_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, J_deriv_bPar_ex ]
implicit none
BEGIN_DOC
! Jastrow variation with respect to parameter b
! we suppose that jast_b_up_up = jast_b_up_dn
END_DOC
double precision :: tmp, Jtmp, a, b, rij
integer :: i, j
b = jast_b_up_up ! and also = jast_b_up_dn
! parallele spin up-up
Jtmp = 0.d0
a = jast_a_up_up
do j = 1, elec_alpha_num-1
!DIR$ LOOP COUNT (50)
do i = j+1, elec_alpha_num
rij = elec_dist(i,j)
tmp = rij/(1.d0+b*rij)
Jtmp = Jtmp + tmp * tmp
enddo
enddo
do j = elec_alpha_num+1, elec_num-1
!DIR$ LOOP COUNT (50)
do i = j+1, elec_num
rij = elec_dist(i,j)
tmp = rij/(1.d0+b*rij)
Jtmp = Jtmp + tmp * tmp
enddo
enddo
J_deriv_bPar_ex = -1.d0 * a * Jtmp
! anti-parallele spin
Jtmp = 0.d0
a = jast_a_up_dn
do j = 1, elec_alpha_num
!DIR$ LOOP COUNT (50)
do i = elec_alpha_num+1, elec_num
rij = elec_dist(i,j)
tmp = rij/(1.d0+b*rij)
Jtmp = Jtmp + tmp * tmp
enddo
enddo
J_deriv_bPar_ex = J_deriv_bPar_ex - a * Jtmp
J_deriv_bPar_ex_min = min(J_deriv_bPar_ex_min, J_deriv_bPar_ex)
J_deriv_bPar_ex_max = max(J_deriv_bPar_ex_max, J_deriv_bPar_ex)
SOFT_TOUCH J_deriv_bPar_ex_min J_deriv_bPar_ex_max
END_PROVIDER
BEGIN_PROVIDER [ double precision, J_deriv_bPar_verif ]
implicit none
BEGIN_DOC
! verification: Jastrow variation with respect to parameter b
! we suppose that jast_b_up_up = jast_b_up_dn
END_DOC
integer :: i
double precision :: eps = 1d-7, der1, der2, pos0
pos0 = eps * jast_b_up_up
! !!!
jast_b_up_up = jast_b_up_up + pos0
TOUCH jast_b_up_up
jast_b_up_dn = jast_b_up_up
TOUCH jast_b_up_dn
der1 = 0.d0
!DIR$ LOOP COUNT (100)
do i = 1, elec_num
der1 += jast_elec_Simple_value(i)
end do
! !!!
jast_b_up_up = jast_b_up_up - 2.d0 * pos0
TOUCH jast_b_up_up
jast_b_up_dn = jast_b_up_up
TOUCH jast_b_up_dn
der2 = 0.d0
!DIR$ LOOP COUNT (100)
do i = 1, elec_num
der2 += jast_elec_Simple_value(i)
end do
! !!!
J_deriv_bPar_verif = 0.5d0 * (der1 - der2) / pos0
J_deriv_bPar_verif_min = min(J_deriv_bPar_verif_min, J_deriv_bPar_verif)
J_deriv_bPar_verif_max = max(J_deriv_bPar_verif_max, J_deriv_bPar_verif)
SOFT_TOUCH J_deriv_bPar_verif_min J_deriv_bPar_verif_max
END_PROVIDER

2
src/PROPERTIES/properties_energy.irp.f
View File

@ -279,5 +279,3 @@ BEGIN_PROVIDER [ double precision, E_loc_zv ]
END_PROVIDER

262
src/QMC_SVD/v0/test_SVD.py Executable file
View File

@ -0,0 +1,262 @@
#!/usr/bin/env python3
# !!!
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# !!!
from ezfio import ezfio
from math import sqrt
from datetime import datetime
import time
import numpy as np
import subprocess
from scipy.linalg import eig, eigh
# PARAMETERS
block_time = 20
eps = 1.
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_energy():
buffer = subprocess.check_output(['qmcchem', 'result', '-e', 'e_loc', filename], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def set_vmc_params():
#subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(20),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# filename])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'None', '-l', str(block_time), filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_svd(n_svd):
# !!!
Ci_h_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_h_matrix_svd = results.find('Ci_h_matrix_svd : [ ') + len( 'Ci_h_matrix_svd : [ ' )
end_Ci_h_matrix_svd = len(results)#results.find('E_loc :')
Ci_h_matrix_svd_buf = results[beg_Ci_h_matrix_svd:end_Ci_h_matrix_svd]
Ci_h_matrix_svd_buf = Ci_h_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_h_matrix_svd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_svd')
stop
else:
#Ci_h_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_h_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_h_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# Ci_h_matrix_svd = np.reshape(Ci_h_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_h_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_svd(n_svd):
# !!!
Ci_overlap_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_overlap_matrix_svd = results.find('Ci_overlap_matrix_svd : [ ') + len( 'Ci_overlap_matrix_svd : [ ' )
end_Ci_overlap_matrix_svd = len(results)#results.find('Ci_h_matrix_svd : [')
Ci_overlap_matrix_svd_buf = results[beg_Ci_overlap_matrix_svd:end_Ci_overlap_matrix_svd]
Ci_overlap_matrix_svd_buf = Ci_overlap_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_overlap_matrix_svd_buf[iline].split()
indc = int( line[0] )
# !!!
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_svd')
stop
# !!!
# !!!
else:
#Ci_overlap_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_overlap_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_overlap_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# !!!
#Ci_overlap_matrix_svd = np.reshape(Ci_overlap_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_overlap_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_postsvd(n_svd):
# !!!
Ci_h_matrix_postsvd = np.zeros( (n_svd*n_svd*n_svd*n_svd) )
# !!!
beg_Ci_h_matrix_postsvd = results.find('Ci_h_matrix_postsvd : [ ') + len( 'Ci_h_matrix_postsvd : [ ' )
end_Ci_h_matrix_postsvd = len(results)
Ci_h_matrix_postsvd_buf = results[beg_Ci_h_matrix_postsvd:end_Ci_h_matrix_postsvd]
Ci_h_matrix_postsvd_buf = Ci_h_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_h_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_postsvd')
stop
else:
Ci_h_matrix_postsvd[indc-1] = float( line[2] )
# !!!
Ci_h_matrix_postsvd = np.reshape(Ci_h_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
return(Ci_h_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_postsvd(n_svd):
# !!!
Ci_overlap_matrix_postsvd = np.zeros( (n_svd*n_svd*n_svd*n_svd) )
# !!!
beg_Ci_overlap_matrix_postsvd = results.find('Ci_overlap_matrix_postsvd : [ ') + len( 'Ci_overlap_matrix_postsvd : [ ' )
end_Ci_overlap_matrix_postsvd = len(results)
Ci_overlap_matrix_postsvd_buf = results[beg_Ci_overlap_matrix_postsvd:end_Ci_overlap_matrix_postsvd]
Ci_overlap_matrix_postsvd_buf = Ci_overlap_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_overlap_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_postsvd')
stop
else:
Ci_overlap_matrix_postsvd[indc-1] = float( line[2] )
# !!!
Ci_overlap_matrix_postsvd = np.reshape(Ci_overlap_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
return(Ci_overlap_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
if __name__ == '__main__':
t0 = time.time()
# !!!
filename = "/home/ammar/qp2/src/svdwf/h2o.ezfio"
ezfio.set_file(filename)
# !!!
print("Today's date:", datetime.now() )
print("filename = {}".format(filename))
print("start QMC:")
#set_vmc_params()
#run_qmc()
#
##stop_qmc()
results = subprocess.check_output(['qmcchem', 'result', filename], encoding='UTF-8')
# !!!
#file = open('results.txt','a')
#file.write('\n \n \n')
#file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#file.write("Today's date: {}\n".format(datetime.now()) )
#file.write("filename = {}\n".format(filename))
#file.write('\n')
#file.write( results )
#file.write('\n')
#print("end QMC after {} minutes\n".format((time.time()-t0)/60.) )
#file.write('+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\n \n')
#file.close()
# !!!
E_loc, ErrEloc = get_energy()
print('Eloc = {} +/- {}'.format(E_loc, ErrEloc))
# !!!
n_svd = 10
Ci_h_matrix_svd = get_Ci_h_matrix_svd(n_svd)
Ci_overlap_matrix_svd = get_Ci_overlap_matrix_svd(n_svd)
# !!!
aa = Ci_h_matrix_svd
bb = Ci_overlap_matrix_svd
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True, check_finite=True, homogeneous_eigvals=False)
print( eigvals_svd+9.194966082434476 )
# !!!
Ci_h_matrix_postsvd = get_Ci_h_matrix_postsvd(n_svd)
Ci_overlap_matrix_postsvd = get_Ci_overlap_matrix_postsvd(n_svd)
# !!!
aa = Ci_h_matrix_postsvd
bb = Ci_overlap_matrix_postsvd
eigvals_postsvd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True, check_finite=True, homogeneous_eigvals=False)
print( eigvals_postsvd+9.194966082434476 )
# !!!
print("end code after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!
# !!!

10
src/QMC_SVD/v1/QR.py Normal file
View File

@ -0,0 +1,10 @@
# !!!
import numpy as np
# !!!
def QR_fact(X):
Q, R = np.linalg.qr(X, mode="reduced")
D = np.diag( np.sign( np.diag(R) ) )
Qunique = np.dot(Q,D)
#Runique = np.dot(D,R)
return(Qunique)
# !!!

20
src/QMC_SVD/v1/RSVD.py Normal file
View File

@ -0,0 +1,20 @@
# !!!
import numpy as np
from QR import QR_fact
# !!!
def powit_RSVD(X, new_r, nb_powit, nb_oversamp):
# !!!
G = np.random.randn(X.shape[1], new_r+nb_oversamp)
Q = QR_fact( np.dot(X,G) )
# !!!
for _ in range(nb_powit):
Q = QR_fact( np.dot(X.T,Q) )
Q = QR_fact( np.dot(X,Q) )
# !!!
Y = np.dot(Q.T,X)
# !!!
U, S, VT = np.linalg.svd(Y, full_matrices=0)
U = np.dot(Q,U)
return U[:,:(new_r)], S[:(new_r)], VT[:(new_r),:]
# !!!
# !!!

513
src/QMC_SVD/v1/diag_after_QMCCHEM.py Executable file
View File

@ -0,0 +1,513 @@
#!/usr/bin/env python3
# !!!
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# !!!
from ezfio import ezfio
from math import sqrt
from datetime import datetime
import time
import numpy as np
import subprocess
from scipy.linalg import eig, eigh
from RSVD import powit_RSVD
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_energy():
buffer = subprocess.check_output(['qmcchem', 'result', '-e', 'e_loc', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def set_vmc_params():
#subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(20),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# EZFIO_file])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'None', '-l', str(block_time), EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_svd():
# !!!
Ci_h_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_h_matrix_svd = results.find('Ci_h_matrix_svd : [ ') + len( 'Ci_h_matrix_svd : [ ' )
end_Ci_h_matrix_svd = len(results)
Ci_h_matrix_svd_buf = results[beg_Ci_h_matrix_svd:end_Ci_h_matrix_svd]
Ci_h_matrix_svd_buf = Ci_h_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_h_matrix_svd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_svd')
stop
else:
#Ci_h_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_h_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_h_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# Ci_h_matrix_svd = np.reshape(Ci_h_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_h_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_svd():
# !!!
Ci_overlap_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_overlap_matrix_svd = results.find('Ci_overlap_matrix_svd : [ ') + len( 'Ci_overlap_matrix_svd : [ ' )
end_Ci_overlap_matrix_svd = len(results)
Ci_overlap_matrix_svd_buf = results[beg_Ci_overlap_matrix_svd:end_Ci_overlap_matrix_svd]
Ci_overlap_matrix_svd_buf = Ci_overlap_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_overlap_matrix_svd_buf[iline].split()
indc = int( line[0] )
# !!!
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_svd')
stop
# !!!
# !!!
else:
#Ci_overlap_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_overlap_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_overlap_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# !!!
#Ci_overlap_matrix_svd = np.reshape(Ci_overlap_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_overlap_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_postsvd():
#file = open('verif_order.txt','w')
# !!!
Ci_h_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_h_matrix_postsvd = results.find('Ci_h_matrix_postsvd : [ ') + len( 'Ci_h_matrix_postsvd : [ ' )
end_Ci_h_matrix_postsvd = len(results)
Ci_h_matrix_postsvd_buf = results[beg_Ci_h_matrix_postsvd:end_Ci_h_matrix_postsvd]
Ci_h_matrix_postsvd_buf = Ci_h_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_h_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_postsvd')
stop
else:
# !!!
kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
#indcrep = kp + (k-1)*n_svd + (lp-1)*n_svd**2 + (l-1)*n_svd**3
#file.write( '{:5} {:5} {:5} {:5} {:5} {:5} \n'.format(indc, indc-indcrep, kp, k, lp, l ) )
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_h_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_h_matrix_postsvd[indc-1] = float( line[2] )
# !!!
#Ci_h_matrix_postsvd = np.reshape(Ci_h_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
#file.close()
return(Ci_h_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_postsvd():
# !!!
Ci_overlap_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_overlap_matrix_postsvd = results.find('Ci_overlap_matrix_postsvd : [ ') + len( 'Ci_overlap_matrix_postsvd : [ ' )
end_Ci_overlap_matrix_postsvd = len(results)
Ci_overlap_matrix_postsvd_buf = results[beg_Ci_overlap_matrix_postsvd:end_Ci_overlap_matrix_postsvd]
Ci_overlap_matrix_postsvd_buf = Ci_overlap_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_overlap_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_postsvd')
stop
else:
# !!!
kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_overlap_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_overlap_matrix_postsvd[indc-1] = float( line[2] )
# !!!
# !!!
#Ci_overlap_matrix_postsvd = np.reshape(Ci_overlap_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
return(Ci_overlap_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def check_symmetric(a, tol=1e-3):
return np.all(np.abs(a-a.T) < tol)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def save_results_to_resultsQMC():
file = open('resultsQMC.txt','a')
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write("Today's date: {}\n".format(datetime.now()))
file.write("EZFIO file = {}\n".format(EZFIO_file))
file.write('\n')
file.write( results )
file.write('\n')
file.write('+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\n \n')
file.close()
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Esvd():
# !!!
# read CI_SVD matrices
Ci_h_matrix_svd = get_Ci_h_matrix_svd()
Ci_overlap_matrix_svd = get_Ci_overlap_matrix_svd()
#print( 'Ci_h_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_svd)) )
#print( 'Ci_overlap_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_svd)) )
# !!!
# symmetrise and diagonalise
aa = Ci_h_matrix_svd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_svd
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
#print( eigvals_svd + E_toadd )
recouvre_svd = np.abs(psi_svd_coeff @ vr)
ind_gssvd = np.argmax(recouvre_svd)
# !!!
E_svd = eigvals_svd[ind_gssvd] + E_toadd
return( E_svd, vr[:,ind_gssvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Epostsvd():
# !!!
# read CI_postSVD matrices
Ci_h_matrix_postsvd = get_Ci_h_matrix_postsvd()
Ci_overlap_matrix_postsvd = get_Ci_overlap_matrix_postsvd()
#print( 'Ci_h_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_postsvd)) )
#print( 'Ci_overlap_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_postsvd)) )
# !!!
# symmetrise and diagonalise
aa = Ci_h_matrix_postsvd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_postsvd
eigvals_postsvd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
#print( eigvals_postsvd + E_toadd )
d_postsvd = np.diagflat(psi_svd_coeff)
d_postsvd = d_postsvd.reshape( (1,n_svd*n_svd) )
recouvre_postsvd = np.abs(d_postsvd @ vr)
ind_gspostsvd = np.argmax(recouvre_postsvd)
#print(recouvre_postsvd, ind_gspostsvd)
# !!!
E_postsvd = eigvals_postsvd[ind_gspostsvd] + E_toadd
# !!!
return( E_postsvd, vr[:,ind_gspostsvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def SVD_postsvd(sigma_postsvd):
# !!!
print( 'performing new SVD for the post SVD eigenvector:' )
# !!!
#sigma_postsvd = sigma_postsvd.reshape( (n_svd,n_svd) )
sigma_postsvd = sigma_postsvd.reshape( n_svd, n_svd, order='F' )
#print( 'sigma_postsvd is symmetric ? {}' .format(check_symmetric(sigma_postsvd)) )
# !!!
# construct the new matrix Y
Y = U_svd @ sigma_postsvd @ V_svd.T
normY = np.linalg.norm(Y, ord='fro')
# !!!
# parameters of RSVD
rank = n_svd
npow = 10
nb_oversamp = 10
# !!!
# call RSV
U_postSVD, sigma_postsvd_diag, VT_postsvd = powit_RSVD(Y, rank, npow, nb_oversamp)
# !!!
# check precision
Y_SVD = np.dot( U_postSVD , np.dot( np.diag(sigma_postsvd_diag) , VT_postsvd ) )
energy = np.sum( np.square(sigma_postsvd_diag) ) / normY**2
err_SVD = 100. * np.linalg.norm( Y - Y_SVD, ord="fro") / normY
print('energy = {}, error = {}\n'.format(energy, err_SVD))
# !!!
return(U_postSVD, sigma_postsvd_diag, VT_postsvd)
# !!!
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_recouv_svd():
recouv_svd = np.abs( sigma0 @ sigma_svd )
return( recouv_svd )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_recouv_postsvd():
d_postsvd = np.diagflat( sigma0 )
d_postsvd = d_postsvd.reshape( (1, n_svd*n_svd) )
recouv_postsvd = np.abs( d_postsvd @ sigma_postsvd )
return( recouv_postsvd )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Hsvd_QP(Hsvd_qp_txt):
Hsvd_qp = np.zeros( (n_svd,n_svd) )
Hsvd_qp_file = open(Hsvd_qp_txt, 'r')
for line in Hsvd_qp_file:
line = line.split()
i = int(line[0]) - 1
j = int(line[1]) - 1
Hsvd_qp[i,j] = float(line[2])
return(Hsvd_qp)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Esvd_QP(Hsvd_qp):
# !!!
# symmetrise and diagonalise
aa = Hsvd_qp
aa = 0.5*( aa + aa.T )
bb = np.identity(n_svd)
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
recouvre_svd = np.abs(psi_svd_coeff @ vr)
ind_gssvd = np.argmax(recouvre_svd)
E_svd = eigvals_svd[ind_gssvd] + E_toadd
return( E_svd, vr[:,ind_gssvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
if __name__ == '__main__':
t0 = time.time()
# !!!
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
EZFIO_file = "/home/ammar/qp2/src/svdwf/h2o_QPsvd.ezfio"
E_toadd = 9.194966082434476 #6.983610961797779
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
# !!!
ezfio.set_file(EZFIO_file)
n_svd = ezfio.get_spindeterminants_n_svd_coefs()
psi_svd_coeff = np.array(ezfio.get_spindeterminants_psi_svd_coefs())
U_svd = np.array(ezfio.get_spindeterminants_psi_svd_alpha())
V_svd = np.array(ezfio.get_spindeterminants_psi_svd_beta())
# !!!
U_svd = U_svd[0,:,:].T
V_svd = V_svd[0,:,:].T
# !!!
print("Today's date:", datetime.now() )
print("EZFIO file = {}".format(EZFIO_file))
print("nuclear energy = {}".format(E_toadd) )
print("n_svd = {} \n".format(n_svd) )
# !!!
#set_vmc_params()
#run_qmc()
#print("start QMC:")
#stop_qmc()
# !!!
print( 'getting QMCCHEM results from {}'.format(EZFIO_file) )
results = subprocess.check_output(['qmcchem', 'result', EZFIO_file], encoding='UTF-8')
# !!!
E_loc, ErrEloc = get_energy()
print('Eloc = {} +/- {}\n'.format(E_loc, ErrEloc))
# !!!
save_resultsQMC = input( 'save QMC results from {}? (y/n) '.format(EZFIO_file) )
if( save_resultsQMC == 'y' ):
print('saving in resultsQMC.txt')
save_results_to_resultsQMC()
print('\n')
# !!!
sigma0 = psi_svd_coeff
# !!!
read_QPsvd = input( 'read QP Hsvd matrix ? (y/n) ')
if( read_QPsvd == 'y' ):
Hsvd_qp_txt = input('name of file with QM H_svd matrix:')
Hsvd_qp = get_Hsvd_QP(Hsvd_qp_txt)
E_svd_QP, _ = get_Esvd_QP(Hsvd_qp)
print('QP SVD enegry = {} \n'.format(E_svd_QP) )
# !!!
E_svd, sigma_svd = get_Esvd()
recouv_svd = get_recouv_svd()
print('QMC=CHEM SVD enegry = {} '.format(E_svd) )
print('QMC=CHEM recouvrement SVD ={} \n'.format(recouv_svd) )
# !!!
E_postsvd, sigma_postsvd = get_Epostsvd()
recouv_postsvd = get_recouv_postsvd()
print('QMC=CHEM post SVD energy = {} '.format(E_postsvd) )
print('QMC=CHEM recouvrement post SVD ={} \n'.format(recouv_postsvd) )
# !!!
save_to_EZFIO = input( "modify EZFIO (with svd or postsvd)? " )
# !!!
if( save_to_EZFIO == 'svd' ):
sigma_SVD_toEZFIO = np.zeros( ( n_svd, 1) )
sigma_SVD_toEZFIO[:,0] = sigma_svd
ezfio.set_spindeterminants_psi_svd_coefs( sigma_SVD_toEZFIO )
# !!!
elif( save_to_EZFIO == 'postsvd' ):
# SVD first
U_postSVD, sigma_postsvd_diag, V_postSVD = SVD_postsvd(sigma_postsvd)
V_postSVD = V_postSVD.T
# save next in ezfio file
sigma_postSVD_toEZFIO = np.zeros( ( n_svd, 1) )
U_postSVD_toEZFIO = np.zeros( ( U_postSVD.shape[0], U_postSVD.shape[1], 1) )
V_postSVD_toEZFIO = np.zeros( ( V_postSVD.shape[0], V_postSVD.shape[1], 1) )
sigma_postSVD_toEZFIO[:,0] = sigma_postsvd_diag
U_postSVD_toEZFIO[:,:,0] = U_postSVD
V_postSVD_toEZFIO[:,:,0] = V_postSVD
#
ezfio.set_spindeterminants_psi_svd_alpha( U_postSVD_toEZFIO )
ezfio.set_spindeterminants_psi_svd_coefs( sigma_postSVD_toEZFIO )
ezfio.set_spindeterminants_psi_svd_beta( V_postSVD_toEZFIO )
# !!!
else:
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
exit()
# !!!
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!
# !!!

75
src/QMC_SVD/v1/save_svd.py Normal file
View File

@ -0,0 +1,75 @@
#!/usr/bin/env python3
# !!!
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# !!!
from ezfio import ezfio
from datetime import datetime
import time
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
file_to_save = 'postsvd_1.txt'
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
if __name__ == '__main__':
# !!!
if input("are you sure you want before saving in {}? (y/n)".format(file_to_save)) != "y":
exit()
# !!!
t0 = time.time()
# !!!
filename = "/home/ammar/qp2/src/svdwf/h2o_pseudo_1_postsvd"
ezfio.set_file(filename)
# !!!
n_svd = ezfio.get_spindeterminants_n_svd_coefs()
d_svd = ezfio.get_spindeterminants_psi_svd_coefs()
u_svd = ezfio.get_spindeterminants_psi_svd_alpha()
v_svd = ezfio.get_spindeterminants_psi_svd_beta()
# !!!
print("Today's date:", datetime.now() )
print("EZFIO filename: {}".format(filename))
# !!!
file = open(file_to_save, 'a')
#
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write("Today's date: {}\n".format(datetime.now()) )
file.write("EZFIO filename = {}\n".format(filename))
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write( 'n_svd :')
file.write( str(n_svd) )
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write( 'd_svd :')
file.write( str(d_svd) )
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write( 'u_svd :')
file.write( str(u_svd) )
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write( 'v_svd :')
file.write( str(v_svd) )
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#
file.write('\n')
file.write('+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\n \n')
#
file.close()
# !!!
print("SVD save in {} after {:.3f} minutes".format( file_to_save, (time.time()-t0)/60.) )
# !!!
# !!!

105
src/det.irp.f
View File

@ -1188,6 +1188,7 @@ END_PROVIDER
ddet = 0.d0
! n_to_do < 2*elec_alpha_num
if (n_to_do < shiftl(elec_alpha_num,1)) then
do while ( n_to_do > 0 )
@ -1251,6 +1252,7 @@ END_PROVIDER
ASSERT (ddet /= 0.d0)
det_alpha_value_curr = ddet
END_PROVIDER
BEGIN_PROVIDER [ double precision, det_beta_value_curr ]
@ -1509,8 +1511,8 @@ END_PROVIDER
DaC = 0.d0
CDb = 0.d0
if (det_num < shiftr(det_alpha_num*det_beta_num,2)) then
!if( det_num .ne. 1 ) then
if( det_num < shiftr(det_alpha_num*det_beta_num,2)) then
det_num4 = iand(det_num,not(3))
!DIR$ VECTOR ALIGNED
do k=1,det_num4,4
@ -1528,7 +1530,6 @@ END_PROVIDER
CDb(i2) = CDb(i2) + det_coef_matrix_values(k+1)*f
CDb(i3) = CDb(i3) + det_coef_matrix_values(k+2)*f
CDb(i4) = CDb(i4) + det_coef_matrix_values(k+3)*f
if ( ((i2-i1) == 1).and.((i3-i1) == 2).and.((i4-i1) == 3) ) then
DaC(j1) = DaC(j1) + det_coef_matrix_values(k)*det_alpha_value(i1) &
+ det_coef_matrix_values(k+1)*det_alpha_value(i1+1) &
@ -1551,54 +1552,74 @@ END_PROVIDER
CDb(i4) = CDb(i4) + det_coef_matrix_values(k+3)*det_beta_value (j4)
endif
enddo
do k=det_num4+1,det_num
i = det_coef_matrix_rows(k)
j = det_coef_matrix_columns(k)
DaC(j) = DaC(j) + det_coef_matrix_values(k)*det_alpha_value(i)
CDb(i) = CDb(i) + det_coef_matrix_values(k)*det_beta_value (j)
enddo
else
! DaC(det_beta_num) = Trans( det_coef_matrix_dense(det_alpha_num,det_beta_num) ) @ det_alpha_value(det_alpha_num)
! DaC(det_beta_num) = Trans( det_coef_matrix_dense(det_alpha_num,det_beta_num) )
! @ det_alpha_value(det_alpha_num)
call dgemv('T',det_alpha_num,det_beta_num,1.d0,det_coef_matrix_dense, &
size(det_coef_matrix_dense,1), det_alpha_value, 1, 0.d0, DaC, 1)
! CDb(det_alpha_num) = det_coef_matrix_dense(det_alpha_num,det_beta_num) @ det_beta_value(det_beta_num)
! CDb(det_alpha_num) = det_coef_matrix_dense(det_alpha_num,det_beta_num)
! @ det_beta_value(det_beta_num)
call dgemv('N',det_alpha_num,det_beta_num,1.d0,det_coef_matrix_dense, &
size(det_coef_matrix_dense,1), det_beta_value, 1, 0.d0, CDb, 1)
endif
!endif
! Value
! -----
psidet_value = 0.d0
do j=1,det_beta_num
psidet_value = psidet_value + det_beta_value(j) * DaC(j)
enddo
if(det_num .eq. 1) then
psidet_value = det_alpha_value_curr * det_beta_value_curr
else
do j=1,det_beta_num
psidet_value = psidet_value + det_beta_value(j) * DaC(j)
enddo
endif
if (psidet_value == 0.d0) then
call abrt(irp_here,'Determinantal component of the wave function is zero.')
endif
psidet_inv = 1.d0/psidet_value
! Gradients
! ---------
! psidet_grad_lapl(4,elec_alpha_num) = det_alpha_grad_lapl(4,elec_alpha_num,det_alpha_num) @ CDb(det_alpha_num)
call dgemv('N',elec_alpha_num*4,det_alpha_num,1.d0, &
det_alpha_grad_lapl, &
size(det_alpha_grad_lapl,1)*size(det_alpha_grad_lapl,2), &
CDb, 1, 0.d0, psidet_grad_lapl, 1)
if (elec_beta_num /= 0) then
call dgemv('N',elec_beta_num*4,det_beta_num,1.d0, &
det_beta_grad_lapl(1,elec_alpha_num+1,1), &
size(det_beta_grad_lapl,1)*size(det_beta_grad_lapl,2), &
DaC, 1, 0.d0, psidet_grad_lapl(1,elec_alpha_num+1), 1)
if(det_num .eq. 1) then
do i = 1, elec_alpha_num
psidet_grad_lapl(1,i) = det_alpha_grad_lapl_curr(1,i) * det_beta_value_curr
psidet_grad_lapl(2,i) = det_alpha_grad_lapl_curr(2,i) * det_beta_value_curr
psidet_grad_lapl(3,i) = det_alpha_grad_lapl_curr(3,i) * det_beta_value_curr
psidet_grad_lapl(4,i) = det_alpha_grad_lapl_curr(4,i) * det_beta_value_curr
enddo
do i = elec_alpha_num+1, elec_num
psidet_grad_lapl(1,i) = det_beta_grad_lapl_curr(1,i) * det_alpha_value_curr
psidet_grad_lapl(2,i) = det_beta_grad_lapl_curr(2,i) * det_alpha_value_curr
psidet_grad_lapl(3,i) = det_beta_grad_lapl_curr(3,i) * det_alpha_value_curr
psidet_grad_lapl(4,i) = det_beta_grad_lapl_curr(4,i) * det_alpha_value_curr
enddo
else
! psidet_grad_lapl(4,elec_alpha_num) =
! det_alpha_grad_lapl(4,elec_alpha_num,det_alpha_num) @ CDb(det_alpha_num)
call dgemv('N',elec_alpha_num*4,det_alpha_num,1.d0, &
det_alpha_grad_lapl, &
size(det_alpha_grad_lapl,1)*size(det_alpha_grad_lapl,2), &
CDb, 1, 0.d0, psidet_grad_lapl, 1)
if (elec_beta_num /= 0) then
call dgemv('N',elec_beta_num*4,det_beta_num,1.d0, &
det_beta_grad_lapl(1,elec_alpha_num+1,1), &
size(det_beta_grad_lapl,1)*size(det_beta_grad_lapl,2), &
DaC, 1, 0.d0, psidet_grad_lapl(1,elec_alpha_num+1), 1)
endif
endif
if (do_pseudo) then
call dgemv('N',elec_alpha_num,det_alpha_num,psidet_inv, &
det_alpha_pseudo, size(det_alpha_pseudo,1), &
@ -1750,7 +1771,8 @@ END_PROVIDER
! !!!
psidet_value_SVD = 0.d0
do l = 1, n_svd_coefs
psidet_value_SVD = psidet_value_SVD + det_beta_value_SVD(l) * psi_svd_coefs(l,1) * det_alpha_value_SVD(l)
psidet_value_SVD = psidet_value_SVD + det_beta_value_SVD(l) &
* psi_svd_coefs(l,1) * det_alpha_value_SVD(l)
enddo
if (psidet_value_SVD == 0.d0) then
call abrt(irp_here,'Determinantal component of the SVD wave function is zero.')
@ -1763,14 +1785,14 @@ END_PROVIDER
! -~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~
! !!!
if (do_pseudo) then
! det_alpha_pseudo_SVD = det_alpha_pseudo @ psi_svd_alpha / psidet_inv_SVD
call dgemm('N', 'N', elec_alpha_num, n_svd_coefs , det_alpha_num, 1.d0 &
! det_alpha_pseudo_SVD = det_alpha_pseudo @ psi_svd_alpha * psidet_inv_SVD
call dgemm('N', 'N', elec_alpha_num, n_svd_coefs , det_alpha_num, psidet_inv_SVD &
, det_alpha_pseudo, size(det_alpha_pseudo,1), psi_svd_alpha(:,:,1), size(psi_svd_alpha,1) &
, 0.d0, det_alpha_pseudo_SVD, size(det_alpha_pseudo_SVD,1) )
! !!!
if (elec_beta_num /= 0) then
! det_beta_pseudo_SVD = det_beta_pseudo @ psi_svd_beta / psidet_inv_SVD
call dgemm('N', 'N', elec_beta_num, n_svd_coefs , det_beta_num, 1.d0 &
! det_beta_pseudo_SVD = det_beta_pseudo @ psi_svd_beta * psidet_inv_SVD
call dgemm('N', 'N', elec_beta_num, n_svd_coefs , det_beta_num, psidet_inv_SVD &
, det_beta_pseudo(elec_alpha_num+1,1), size(det_beta_pseudo,1), psi_svd_beta(:,:,1), size(psi_svd_beta,1) &
, 0.d0, det_beta_pseudo_SVD(elec_alpha_num+1,1), size(det_beta_pseudo_SVD,1) )
endif
@ -1832,13 +1854,15 @@ END_PROVIDER
! !!!
do mm = 1, 4
! !!!
call dgemm('N', 'N', elec_alpha_num, n_svd_coefs , det_alpha_num, 1.d0 &
, det_alpha_grad_lapl(mm,:,:), size(det_alpha_grad_lapl,2), psi_svd_alpha(:,:,1), size(psi_svd_alpha,1) &
call dgemm('N', 'N', elec_alpha_num, n_svd_coefs, det_alpha_num, 1.d0 &
, det_alpha_grad_lapl(mm,:,:), size(det_alpha_grad_lapl,2) &
, psi_svd_alpha(:,:,1), size(psi_svd_alpha,1) &
, 0.d0, det_alpha_grad_lapl_SVD(mm,:,:), size(det_alpha_grad_lapl_SVD,2) )
! !!!
if (elec_beta_num /= 0) then
call dgemm('N', 'N', elec_beta_num, n_svd_coefs , det_beta_num, 1.d0 &
, det_beta_grad_lapl(mm,:,:), size(det_beta_grad_lapl,2), psi_svd_beta(:,:,1), size(psi_svd_beta,1) &
call dgemm('N', 'N', elec_beta_num, n_svd_coefs, det_beta_num, 1.d0 &
, det_beta_grad_lapl(mm,:,:), size(det_beta_grad_lapl,2) &
, psi_svd_beta(:,:,1), size(psi_svd_beta,1) &
, 0.d0, det_beta_grad_lapl_SVD(mm,:,:), size(det_beta_grad_lapl_SVD,2) )
endif
! !!!
@ -1905,7 +1929,8 @@ END_PROVIDER
do ee = 1, elec_alpha_num
tmp = 0.d0
do l = 1, n_svd_coefs
tmp = tmp + det_alpha_grad_lapl_SVD(mm,ee,l) * psi_svd_coefs(l,1) * det_beta_value_SVD(l)
tmp = tmp + det_alpha_grad_lapl_SVD(mm,ee,l) * psi_svd_coefs(l,1) &
* det_beta_value_SVD(l)
enddo
psidet_grad_lapl_SVD(mm,ee) = tmp
enddo
@ -1914,7 +1939,8 @@ END_PROVIDER
do ee = elec_alpha_num+1, elec_num
tmp = 0.d0
do l = 1, n_svd_coefs
tmp = tmp + det_alpha_value_SVD(l) * psi_svd_coefs(l,1) * det_beta_grad_lapl_SVD(mm,ee,l)
tmp = tmp + det_alpha_value_SVD(l) * psi_svd_coefs(l,1) &
* det_beta_grad_lapl_SVD(mm,ee,l)
enddo
psidet_grad_lapl_SVD(mm,ee) = tmp
enddo
@ -1934,7 +1960,7 @@ END_PROVIDER
do l = 1, n_svd_coefs
tmp = tmp + det_alpha_pseudo_SVD(ee,l) * psi_svd_coefs(l,1) * det_beta_value_SVD(l)
enddo
pseudo_non_local_SVD(ee) = tmp * psi_value_inv_svd
pseudo_non_local_SVD(ee) = tmp * psidet_inv_SVD
enddo
! !!!
if (elec_beta_num /= 0) then
@ -1943,7 +1969,7 @@ END_PROVIDER
do l = 1, n_svd_coefs
tmp = tmp + det_alpha_value_SVD(l) * psi_svd_coefs(l,1) * det_beta_pseudo_SVD(ee,l)
enddo
pseudo_non_local_SVD(ee) = tmp * psi_value_inv_svd
pseudo_non_local_SVD(ee) = tmp * psidet_inv_SVD
enddo
endif
! !!!
@ -2052,7 +2078,8 @@ BEGIN_PROVIDER [ double precision, det_alpha_grad_lapl_curr, (4,elec_alpha_num)
! imo = mo_list_alpha_curr(j)
! do i=1,elec_alpha_num
! do k=1,4
! det_alpha_grad_lapl_curr(k,i) = det_alpha_grad_lapl_curr(k,i) + mo_grad_lapl_alpha(k,i,imo)*slater_matrix_alpha_inv_det(i,j)
! det_alpha_grad_lapl_curr(k,i) = det_alpha_grad_lapl_curr(k,i) + &
! mo_grad_lapl_alpha(k,i,imo)*slater_matrix_alpha_inv_det(i,j)
! enddo
! enddo
! enddo

253
src/opt_Jast/opt_jast.py Normal file
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@ -0,0 +1,253 @@
#!/usr/bin/env python3
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
from ezfio import ezfio
from datetime import datetime
import time
import numpy as np
import subprocess
import atexit
import scipy as sp
import scipy.optimize
from math import sqrt
#------------------------------------------------------------------------------
def make_atom_map():
labels = {}
dimension = 0
# i: label of nuclei
# k: counter of nuclei
for i,k in enumerate(ezfio.nuclei_nucl_label):
if k in labels:
labels[k].append(i)
else:
labels[k] = [dimension, i]
dimension += 1
atom_map = [[] for i in range(dimension)]
for atom in labels.keys():
l = labels[atom]
atom_map[l[0]] = l[1:]
return atom_map
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_pen():
d = ezfio.jastrow_jast_pen
return np.array([d[m[0]] for m in atom_map])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_pen(x):
#x = np.abs(x)
y = list(ezfio.jastrow_jast_pen)
for i,m in enumerate(atom_map):
for j in m:
y[j] = x[i]
ezfio.set_jastrow_jast_pen(y)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_b():
b = ezfio.get_jastrow_jast_b_up_up()
return b
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_b(b):
ezfio.set_jastrow_jast_b_up_up(b)
ezfio.set_jastrow_jast_b_up_dn(b)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_energy():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_variance():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc_qmcvar', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, variance, error = [float(x) for x in buffer.split()]
return variance, error
else:
return None, None
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_vmc_params(block_time,total_time):
#subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(block_time),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# EZFIO_file])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
'-t', str(total_time),
'-l', str(block_time), EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def f(x):
# !!!
print('f on:')
print('nuc param Jast = {}'.format(x[:-1]))
print('b param Jast = {}'.format(x[-1]))
# !!!
global i_fev
i_fev = i_fev + 1
# !!!
global memo_energy
# !!!
print ("x = %s"%str(x))
h = str(x)
if h in memo_energy:
return memo_energy[h]
# !!!
set_params_pen(x[:-1])
set_params_b(x[-1])
set_params_pen(x)
set_vmc_params(block_time_f, total_time_f)
# !!!
pid = os.fork()
if pid == 0:
run_qmc()
os._exit(os.EX_OK)
else:
atexit.register(stop_qmc)
time.sleep(3.*block_time_f/4.)
local_thresh = thresh
err = thresh+1.
ii = 1
ii_max = int(total_time_f/block_time_f) - 1
while( (err > local_thresh) and (ii<ii_max) ):
time.sleep(block_time_f)
e, e_err = get_energy()
variance, v_err = get_variance()
if e is None or variance is None:
continue
energy = e + variance # minimise energy + variance
err = sqrt(e_err*e_err+v_err*v_err)
print(" energy: %f %f "%(e, e_err))
print(" varian: %f %f "%(variance, v_err))
print(" additi: %f %f "%(energy, err))
print(" ")
if (energy-2.*err) > memo_energy['fmin']+thresh:
local_thresh = 10.*thresh
elif (energy+2.*err) < memo_energy['fmin']-thresh:
local_thresh = 10.*thresh
ii = ii + 1
# Check if PID is still running
try:
os.kill(pid,0)
except OSError:
print("---")
break
stop_qmc()
# !!!
os.wait()
memo_energy[h] = energy + err
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
# !!!
return energy
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
if __name__ == '__main__':
t0 = time.time()
# !!!
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
EZFIO_file = "/home/ammar/qp2/src/svdwf/h2o_optJast"
# nuclear energy
E_toadd = 9.194966082434476
# PARAMETERS
thresh = 1.e-2
# maximum allowed number of function evaluations
N_fev = 4
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
# !!!
ezfio.set_file(EZFIO_file)
print("Today's date:", datetime.now() )
print("EZFIO file = {}".format(EZFIO_file))
# !!!
# map nuclei to a list
# for H2O this will give: atom_map = [[0], [1, 2]]
atom_map = make_atom_map()
n_nucpar = len(atom_map) # nb of nclear parameters
# !!!
# x = get_params_pen()
x = [1.25816521, 0.23766714]
print('initial pen: {}'.format(x))
b_par = get_params_b()
print('initial b: {}'.format(b_par))
x.append(b_par)
# !!!
i_fev = 0
bnds = [(0.001, 9.99) for _ in range(n_nucpar)]
memo_energy = {'fmin': 100000000.}
opt = sp.optimize.minimize(f, x, method="Powell", bounds=bnds
, options= {'disp':True,
'ftol':thresh,
'xtol':0.2,
'maxfev':N_fev} )
print("x = "+str(opt))
set_params_pen(opt['x'])
print('number of function evaluations = {}'.format(i_fev))
# !!!
print('memo_energy: {}'.format(memo_energy))
# !!!
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!

171
src/opt_Jast/opt_jast_Anthony.py Normal file
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@ -0,0 +1,171 @@
#!/usr/bin/env python3
import scipy as sp
import scipy.optimize
import numpy as np
import sys
import os
import time
import subprocess
from math import sqrt
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
from ezfio import ezfio
# PARAMETERS
thresh = 1.e-2
block_time = 20
def main():
if len(sys.argv) != 2:
print("Usage: %s <EZFIO_DIRECTORY>"%sys.argv[0])
sys.exti(1)
filename = sys.argv[1]
ezfio.set_file(filename)
def make_atom_map():
labels = {}
dimension = 0
for i,k in enumerate(ezfio.nuclei_nucl_label):
if k in labels:
labels[k].append(i)
else:
labels[k] = [dimension, i]
dimension += 1
atom_map = [[] for i in range(dimension)]
for atom in labels.keys():
l = labels[atom]
atom_map[l[0]] = l[1:]
return atom_map
atom_map = make_atom_map()
def get_params_pen():
d = ezfio.jastrow_jast_pen
return np.array([d[m[0]] for m in atom_map])
def get_energy():
buffer = subprocess.check_output(['qmcchem', 'result', '-e', 'e_loc', filename],
encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
def get_variance():
buffer = subprocess.check_output(['qmcchem', 'result', '-e',
'e_loc_qmcvar', filename],
encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, variance, error = [float(x) for x in buffer.split()]
return variance, error
else:
return None, None
def set_params_pen(x):
x = np.abs(x)
y=list(ezfio.jastrow_jast_pen)
for i,m in enumerate(atom_map):
for j in m:
y[j] = x[i]
ezfio.set_jastrow_jast_pen(y)
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', filename])
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', filename])
def set_vmc_params():
# subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(block_time),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# filename])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
'-l', str(block_time),
filename])
memo_energy = {'fmin': 100000000.}
def f(x):
print ("x = %s"%str(x))
h = str(x)
if h in memo_energy:
return memo_energy[h]
set_params_pen(x)
set_vmc_params()
pid = os.fork()
if pid == 0:
run_qmc()
os._exit(os.EX_OK)
else:
import atexit
atexit.register(stop_qmc)
err = thresh+1.
time.sleep(3.*block_time/4.)
local_thresh = thresh
while err > local_thresh:
time.sleep(block_time)
e, e_err = get_energy()
variance, v_err = get_variance()
if e is None or variance is None:
continue
energy = e + variance
err = sqrt(e_err*e_err+v_err*v_err)
print(" %f %f %f %f %f %f"%(e, e_err, variance, v_err, energy, err))
if (energy-2.*err) > memo_energy['fmin']+thresh:
local_thresh = 10.*thresh
elif (energy+2.*err) < memo_energy['fmin']-thresh:
local_thresh = 10.*thresh
# Check if PID is still running
try:
os.kill(pid,0)
except OSError:
print("---")
break
stop_qmc()
os.wait()
memo_energy[h] = energy + err
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
return energy
def run():
x = get_params_pen()
if sum(x) == 0.:
jast_a_up_dn = ezfio.jastrow_jast_a_up_dn
x += jast_a_up_dn
opt = sp.optimize.minimize(f,x,method="Powell",
options= {'disp':True, 'ftol':thresh,'xtol':0.02})
print("x = "+str(opt))
set_params_pen(opt['x'])
run()
if __name__ == '__main__':
main()

225
src/opt_Jast/opt_jast_freegrad.py Normal file
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@ -0,0 +1,225 @@
#!/usr/bin/env python3
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
from ezfio import ezfio
from datetime import datetime
import time
import numpy as np
import subprocess
import atexit
import scipy as sp
import scipy.optimize
from math import sqrt
#------------------------------------------------------------------------------
def make_atom_map():
labels = {}
dimension = 0
# i: label of nuclei
# k: counter of nuclei
for i,k in enumerate(ezfio.nuclei_nucl_label):
if k in labels:
labels[k].append(i)
else:
labels[k] = [dimension, i]
dimension += 1
atom_map = [[] for i in range(dimension)]
for atom in labels.keys():
l = labels[atom]
atom_map[l[0]] = l[1:]
return atom_map
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_pen():
d = ezfio.jastrow_jast_pen
return np.array([d[m[0]] for m in atom_map])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_pen(x):
y = list(ezfio.jastrow_jast_pen)
for i,m in enumerate(atom_map):
for j in m:
y[j] = x[i]
ezfio.set_jastrow_jast_pen(y)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_b():
b = ezfio.get_jastrow_jast_b_up_up()
return b
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_b(b):
ezfio.set_jastrow_jast_b_up_up(b)
ezfio.set_jastrow_jast_b_up_dn(b)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_energy():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_variance():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc_qmcvar', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, variance, error = [float(x) for x in buffer.split()]
return variance, error
else:
return None, None
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_vmc_params(block_time,total_time):
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
'-t', str(total_time),
'-l', str(block_time), EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def f(x):
# !!!
global i_fev
global memo_energy
print(' eval {} of f on:'.format(i_fev))
print(' nuc param Jast = {}'.format(x[:-1]))
print(' b param Jast = {}'.format(x[-1]))
h = str(x)
if h in memo_energy:
return memo_energy[h]
# !!!
i_fev = i_fev + 1
# !!!
set_params_pen(x[:-1])
set_params_b(x[-1])
block_time_f = 30
total_time_f = 65
set_vmc_params(block_time_f, total_time_f)
# !!!
loc_err = 10.
ii = 0
ii_max = 5
energy = None
err = None
while( thresh < loc_err ):
run_qmc()
energy, err = get_energy()
if( (energy is None) or (err is None) ):
continue
elif( memo_energy['fmin'] < (energy-2.*err) ):
print(" %d energy: %f %f "%(ii, energy, err))
break
else:
loc_err = err
ii = ii + 1
print(" %d energy: %f %f "%(ii, energy, err))
if( ii_max < ii ):
break
print(" ")
# !!!
memo_energy[h] = energy + err
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
# !!!
return energy
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
if __name__ == '__main__':
# !!!
t0 = time.time()
# !!!
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
EZFIO_file = "/home/ammar/qp2/src/svdwf/h2o_optJast"
# PARAMETERS
thresh = 1.e-2
# maximum allowed number of function evaluations
N_fev = 4
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
# !!!
ezfio.set_file(EZFIO_file)
print(" Today's date:", datetime.now() )
print(" EZFIO file = {}".format(EZFIO_file))
# !!!
# map nuclei to a list
# for H2O this will give: atom_map = [[0], [1, 2]]
atom_map = make_atom_map()
n_par = len(atom_map) # nb of nclear parameters
n_par = n_par + 1 # e-e parameter b
# !!!
# x = get_params_pen()
x = [1.29386006, 0.21362821]
print(' initial pen: {}'.format(x))
#b_par = get_params_b()
b_par = 1.5291090863304375
print(' initial b: {}'.format(b_par))
x.append(b_par)
# !!!
i_fev = 1
bnds = [(0.001, 9.99) for _ in range(n_par)]
memo_energy = {'fmin': 100.}
opt = sp.optimize.minimize(f, x, method="Powell", bounds=bnds
, options= {'disp':True,
'ftol':0.2,
'xtol':0.2,
'maxfev':5} )
print(" x = "+str(opt))
set_params_pen(opt['x'])
print(' number of function evaluations = {}'.format(i_fev))
# !!!
print(' memo_energy: {}'.format(memo_energy))
# !!!
print(" end after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!

301
src/opt_Jast/opt_jast_grad.py Normal file
View File

@ -0,0 +1,301 @@
#!/usr/bin/env python3
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
from ezfio import ezfio
from datetime import datetime
import time
import numpy as np
import subprocess
import atexit
import scipy as sp
import scipy.optimize
from math import sqrt
#------------------------------------------------------------------------------
def make_atom_map():
labels = {}
dimension = 0
# i: label of nuclei
# k: counter of nuclei
for i,k in enumerate(ezfio.nuclei_nucl_label):
if k in labels:
labels[k].append(i)
else:
labels[k] = [dimension, i]
dimension += 1
atom_map = [[] for i in range(dimension)]
for atom in labels.keys():
l = labels[atom]
atom_map[l[0]] = l[1:]
return atom_map
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_pen():
d = ezfio.jastrow_jast_pen
return np.array([d[m[0]] for m in atom_map])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_pen(x):
y = list(ezfio.jastrow_jast_pen)
for i,m in enumerate(atom_map):
for j in m:
y[j] = x[i]
ezfio.set_jastrow_jast_pen(y)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_params_b():
b = ezfio.get_jastrow_jast_b_up_up()
return b
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_params_b(b):
ezfio.set_jastrow_jast_b_up_up(b)
ezfio.set_jastrow_jast_b_up_dn(b)
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_energy():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc', EZFIO_file], encoding='UTF-8')
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_variance():
buffer = subprocess.check_output(
['qmcchem', 'result', '-e', 'e_loc_qmcvar', EZFIO_file], encoding='UTF-8')
buffer = buffer.splitlines()[-1]
_, variance, error = [float(x) for x in buffer.split()]
return variance, error
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_energy_deriv_nucPar():
# !!!
buffer = subprocess.check_output(
['qmcchem', 'result', EZFIO_file], encoding='UTF-8')
end = len(buffer)
# !!!
deriv_nucPar1 = []
beg = buffer.find('E_deriv_nucpar_loc1 : [ ')
beg = beg + len( 'E_deriv_nucpar_loc1 : [ ' )
der_buf = buffer[beg:end]
der_buf = der_buf.split( '\n' )
for iline in range(1, n_nucpar+1):
line = der_buf[iline].split()
deriv_nucPar1.append( float(line[2]) )
# !!!
deriv_nucPar2 = []
beg = buffer.find('E_deriv_nucpar_loc2 : [ ')
beg = beg + len( 'E_deriv_nucpar_loc2 : [ ' )
der_buf = buffer[beg:end]
der_buf = der_buf.split( '\n' )
for iline in range(1, n_nucpar+1):
line = der_buf[iline].split()
deriv_nucPar2.append( float(line[2]) )
# !!!
deriv_nucPar = []
e, _ = get_energy()
for i in range(n_nucpar):
tmp = 2. * ( deriv_nucPar1[i] - e * deriv_nucPar2[i] )
deriv_nucPar.append( tmp )
# !!!
return deriv_nucPar
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def get_energy_deriv_bPar():
# !!!
buffer = subprocess.check_output(
['qmcchem', 'result', EZFIO_file], encoding='UTF-8')
end = len(buffer)
# !!!
beg = buffer.find('E_deriv_bpar_loc1 : ')
beg = beg + len( 'E_deriv_bpar_loc1 : ' )
der_buf = buffer[beg:end]
der_buf = der_buf.split( '\n' )
der_buf = der_buf[0].split()
deriv_bPar1 = float(der_buf[0])
# !!!
beg = buffer.find('E_deriv_bpar_loc2 : ')
beg = beg + len( 'E_deriv_bpar_loc2 : ' )
der_buf = buffer[beg:end]
der_buf = der_buf.split( '\n' )
der_buf = der_buf[0].split()
deriv_bPar2 = float(der_buf[0])
# !!!
e, _ = get_energy()
deriv_bPar = deriv_bPar1 - e * deriv_bPar2
# !!!
return deriv_bPar
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def set_vmc_params(block_time,total_time):
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
'-t', str(total_time),
'-l', str(block_time), EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', EZFIO_file])
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def f(x):
# !!!
print('f on:')
print('nuc param Jast = {}'.format(x[:-1]))
print('b param Jast = {}'.format(x[-1]))
# !!!
global i_fev
i_fev = i_fev + 1
# !!!
set_params_pen(x[:-1])
set_params_b(x[-1])
block_time_f = 20
total_time_f = 40
set_vmc_params(block_time_f, total_time_f)
# !!!
err = 10.
ii = 0
ii_max = 5
while( (err > thresh) and (ii<ii_max) ):
ii = ii + 1
run_qmc()
energy, err = get_energy()
print(" energy: %f %f "%(energy, err))
print(" ")
# !!!
global memo_energy
h = str(x)
memo_energy[h] = energy + err
memo_energy['fmin'] = min(energy, memo_energy['fmin'])
# !!!
return energy
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
def fprime(x):
# !!!
# used with CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg,
# trust-krylov, trust-exact, trust-constr
# !!!
print('derivative on:')
print('nuc param Jast = {}'.format(x[:-1]))
print('b param Jast = {}'.format(x[-1]))
# !!!
set_params_pen(x[:-1])
set_params_b(x[-1])
block_time_fp = 20
total_time_fp = 30
set_vmc_params(block_time_fp, total_time_fp)
run_qmc()
# !!!
fp = get_energy_deriv_nucPar()
print('nuc param Jast = {}'.format(fp))
fp_bpar = get_energy_deriv_bPar()
print('b param Jast = {}'.format(fp_bpar))
fp.append(fp_bpar)
print(" ")
# !!!
return fp
#------------------------------------------------------------------------------
##
###
##
#------------------------------------------------------------------------------
if __name__ == '__main__':
# !!!
t0 = time.time()
# !!!
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
EZFIO_file = "/home/ammar/qp2/src/svdwf/h2o_optJast"
# nuclear energy
E_toadd = 9.194966082434476
# PARAMETERS
thresh = 1.e-2
# maximum allowed number of function evaluations
N_fev = 5
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
# !!!
ezfio.set_file(EZFIO_file)
print("Today's date:", datetime.now() )
print("EZFIO file = {}".format(EZFIO_file))
# !!!
# map nuclei to a list
# for H2O this will give: atom_map = [[0], [1, 2]]
atom_map = make_atom_map()
n_nucpar = len(atom_map) # nb of nclear parameters
# !!!
# x = get_params_pen()
x = [1.25816521, 0.35]
print('initial pen: {}'.format(x))
b_par = get_params_b()
print('initial b: {}'.format(b_par))
x.append(b_par)
# !!!
#i_fev = 0
#bnds = [(0.001, 9.99) for _ in range(n_nucpar)]
#memo_energy = {'fmin': 100000000.}
#opt = sp.optimize.minimize(f, x, method="Powell", bounds=bnds
# , options= {'disp':True,
# 'ftol':thresh,
# 'xtol':0.2,
# 'maxfev':N_fev} )
#print("x = "+str(opt))
#set_params_pen(opt['x'])
#print('number of function evaluations = {}'.format(i_fev))
# !!!
#print('memo_energy: {}'.format(memo_energy))
# !!!
#stop_qmc()
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!

4
src/prepare_walkers.irp.f
View File

@ -15,8 +15,8 @@ subroutine draw_init_points
allocate (do_elec(elec_num), xmin(3,elec_num))
xmin = -huge(1.)
norm = 0.
do i=1,elec_alpha_num
do j=1,ao_num
do j = 1, ao_num
do i = 1, elec_alpha_num
norm += mo_coef_transp(i,j)*mo_coef_transp(i,j)
enddo
enddo

325
src/test_SVD/QMCCHEM_withSVD.py Executable file
View File

@ -0,0 +1,325 @@
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# !!!
from ezfio import ezfio
from math import sqrt
from datetime import datetime
import time
import numpy as np
import subprocess
from scipy.linalg import eig, eigh
# PARAMETERS
block_time = 20
eps = 1.
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_energy():
buffer = subprocess.check_output(['qmcchem', 'result', '-e', 'e_loc', filename], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def set_vmc_params():
#subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(20),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# filename])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'None', '-l', str(block_time), filename])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_svd(n_svd):
# !!!
Ci_h_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_h_matrix_svd = results.find('Ci_h_matrix_svd : [ ') + len( 'Ci_h_matrix_svd : [ ' )
end_Ci_h_matrix_svd = len(results)#results.find('E_loc :')
Ci_h_matrix_svd_buf = results[beg_Ci_h_matrix_svd:end_Ci_h_matrix_svd]
Ci_h_matrix_svd_buf = Ci_h_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_h_matrix_svd_buf[iline].split()
#print(line)
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_svd')
stop
else:
#Ci_h_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_h_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_h_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# Ci_h_matrix_svd = np.reshape(Ci_h_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_h_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_svd(n_svd):
# !!!
Ci_overlap_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_overlap_matrix_svd = results.find('Ci_overlap_matrix_svd : [ ') + len( 'Ci_overlap_matrix_svd : [ ' )
end_Ci_overlap_matrix_svd = len(results)#results.find('Ci_h_matrix_svd : [')
Ci_overlap_matrix_svd_buf = results[beg_Ci_overlap_matrix_svd:end_Ci_overlap_matrix_svd]
Ci_overlap_matrix_svd_buf = Ci_overlap_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_overlap_matrix_svd_buf[iline].split()
indc = int( line[0] )
# !!!
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_svd')
stop
# !!!
# !!!
else:
#Ci_overlap_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_overlap_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_overlap_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# !!!
#Ci_overlap_matrix_svd = np.reshape(Ci_overlap_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_overlap_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_postsvd(n_svd):
#file = open('verif_order.txt','w')
# !!!
Ci_h_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_h_matrix_postsvd = results.find('Ci_h_matrix_postsvd : [ ') + len( 'Ci_h_matrix_postsvd : [ ' )
end_Ci_h_matrix_postsvd = len(results)
Ci_h_matrix_postsvd_buf = results[beg_Ci_h_matrix_postsvd:end_Ci_h_matrix_postsvd]
Ci_h_matrix_postsvd_buf = Ci_h_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_h_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_postsvd')
stop
else:
# !!!
kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
#indcrep = kp + (k-1)*n_svd + (lp-1)*n_svd**2 + (l-1)*n_svd**3
#file.write( '{:5} {:5} {:5} {:5} {:5} {:5} \n'.format(indc, indc-indcrep, kp, k, lp, l ) )
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_h_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_h_matrix_postsvd[indc-1] = float( line[2] )
# !!!
#Ci_h_matrix_postsvd = np.reshape(Ci_h_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
#file.close()
return(Ci_h_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_postsvd(n_svd):
# !!!
Ci_overlap_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_overlap_matrix_postsvd = results.find('Ci_overlap_matrix_postsvd : [ ') + len( 'Ci_overlap_matrix_postsvd : [ ' )
end_Ci_overlap_matrix_postsvd = len(results)
Ci_overlap_matrix_postsvd_buf = results[beg_Ci_overlap_matrix_postsvd:end_Ci_overlap_matrix_postsvd]
Ci_overlap_matrix_postsvd_buf = Ci_overlap_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_overlap_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_postsvd')
stop
else:
# !!!
kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_overlap_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_overlap_matrix_postsvd[indc-1] = float( line[2] )
# !!!
# !!!
#Ci_overlap_matrix_postsvd = np.reshape(Ci_overlap_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
return(Ci_overlap_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def check_symmetric(a, tol=1e-3):
return np.all(np.abs(a-a.T) < tol)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
if __name__ == '__main__':
t0 = time.time()
# !!!
filename = "/home/aammar/qp2/src/svdwf/h2o_pseudo"
ezfio.set_file(filename)
# !!!
psi_svd_coeff = np.array(ezfio.get_spindeterminants_psi_svd_coefs())
U_svd = np.array(ezfio.get_spindeterminants_psi_svd_alpha())
V_svd = np.array(ezfio.get_spindeterminants_psi_svd_beta())
# !!!
print("Today's date:", datetime.now() )
print("filename = {}".format(filename))
# !!!
#set_vmc_params()
#run_qmc()
#print("start QMC:")
#stop_qmc()
# !!!
results = subprocess.check_output(['qmcchem', 'result', filename], encoding='UTF-8')
# !!!
#file = open('results.txt','a')
#file.write('\n \n \n')
#file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
#file.write("Today's date: {}\n".format(datetime.now()) )
#file.write("filename = {}\n".format(filename))
#file.write('\n')
#file.write( results )
#file.write('\n')
#file.write('+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\n \n')
#file.close()
# !!!
E_loc, ErrEloc = get_energy()
print('Eloc = {} +/- {}'.format(E_loc, ErrEloc))
# !!!
n_svd = 10
E_toadd = 6.983610961797779
# !!!
Ci_h_matrix_svd = get_Ci_h_matrix_svd(n_svd)
#print( 'Ci_h_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_svd)) )
Ci_overlap_matrix_svd = get_Ci_overlap_matrix_svd(n_svd)
#print( 'Ci_overlap_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_svd)) )
# !!!
aa = Ci_h_matrix_svd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_svd
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True, check_finite=True, homogeneous_eigvals=False)
print( eigvals_svd + E_toadd )
# !!!
recouvre_svd = np.abs(psi_svd_coeff @ vr)
ind_gssvd = np.argmax(recouvre_svd)
print('svd : ', ind_gssvd, eigvals_svd[ind_gssvd] + E_toadd )
# !!!
Ci_h_matrix_postsvd = get_Ci_h_matrix_postsvd(n_svd)
#print( 'Ci_h_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_postsvd)) )
Ci_overlap_matrix_postsvd = get_Ci_overlap_matrix_postsvd(n_svd)
#print( 'Ci_overlap_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_postsvd)) )
# !!!
aa = Ci_h_matrix_postsvd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_postsvd
eigvals_postsvd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True, check_finite=True, homogeneous_eigvals=False)
print( eigvals_postsvd + E_toadd )
# !!!
d_postsvd = np.diagflat(psi_svd_coeff)
d_postsvd = d_postsvd.reshape( (1,n_svd*n_svd) )
recouvre_postsvd = np.abs(d_postsvd @ vr)
ind_gspostsvd = np.argmax(recouvre_postsvd)
print('post svd :', ind_gspostsvd, eigvals_postsvd[ind_gspostsvd]+E_toadd )
# !!!
print("end code after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!
# !!!

510
src/test_SVD/h2o/QMCCHEM_withSVD.py Executable file
View File

@ -0,0 +1,510 @@
# !!!
import sys, os
QMCCHEM_PATH=os.environ["QMCCHEM_PATH"]
sys.path.insert(0,QMCCHEM_PATH+"/EZFIO/Python/")
# !!!
from ezfio import ezfio
from math import sqrt
from datetime import datetime
import time
import numpy as np
import subprocess
from scipy.linalg import eig, eigh
from RSVD import powit_RSVD
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_energy():
buffer = subprocess.check_output(['qmcchem', 'result', '-e', 'e_loc', EZFIO_file], encoding='UTF-8')
if buffer.strip() != "":
buffer = buffer.splitlines()[-1]
_, energy, error = [float(x) for x in buffer.split()]
return energy, error
else:
return None, None
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def run_qmc():
return subprocess.check_output(['qmcchem', 'run', EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def stop_qmc():
subprocess.check_output(['qmcchem', 'stop', EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def set_vmc_params():
#subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'Simple',
# '-m', 'VMC',
# '-l', str(20),
# '--time-step=0.3',
# '--stop-time=36000',
# '--norm=1.e-5',
# '-w', '10',
# EZFIO_file])
subprocess.check_output(['qmcchem', 'edit', '-c', '-j', 'None', '-l', str(block_time), EZFIO_file])
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_svd():
# !!!
Ci_h_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_h_matrix_svd = results.find('Ci_h_matrix_svd : [ ') + len( 'Ci_h_matrix_svd : [ ' )
end_Ci_h_matrix_svd = len(results)
Ci_h_matrix_svd_buf = results[beg_Ci_h_matrix_svd:end_Ci_h_matrix_svd]
Ci_h_matrix_svd_buf = Ci_h_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_h_matrix_svd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_svd')
stop
else:
#Ci_h_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_h_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_h_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# Ci_h_matrix_svd = np.reshape(Ci_h_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_h_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_svd():
# !!!
Ci_overlap_matrix_svd = np.zeros( (n_svd,n_svd) )
# !!!
beg_Ci_overlap_matrix_svd = results.find('Ci_overlap_matrix_svd : [ ') + len( 'Ci_overlap_matrix_svd : [ ' )
end_Ci_overlap_matrix_svd = len(results)
Ci_overlap_matrix_svd_buf = results[beg_Ci_overlap_matrix_svd:end_Ci_overlap_matrix_svd]
Ci_overlap_matrix_svd_buf = Ci_overlap_matrix_svd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**2+1):
# !!!
line = Ci_overlap_matrix_svd_buf[iline].split()
indc = int( line[0] )
# !!!
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_svd')
stop
# !!!
# !!!
else:
#Ci_overlap_matrix_svd[indc-1] = float( line[2] )
irow = indc % n_svd
icol = indc // n_svd
if( irow!=0 ):
Ci_overlap_matrix_svd[irow-1][icol] = float( line[2] )
else:
Ci_overlap_matrix_svd[n_svd-1][icol-1] = float( line[2] )
# !!!
# !!!
# !!!
#Ci_overlap_matrix_svd = np.reshape(Ci_overlap_matrix_svd, (n_svd, n_svd), order='F')
# !!!
return(Ci_overlap_matrix_svd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_h_matrix_postsvd():
#file = open('verif_order.txt','w')
# !!!
Ci_h_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_h_matrix_postsvd = results.find('Ci_h_matrix_postsvd : [ ') + len( 'Ci_h_matrix_postsvd : [ ' )
end_Ci_h_matrix_postsvd = len(results)
Ci_h_matrix_postsvd_buf = results[beg_Ci_h_matrix_postsvd:end_Ci_h_matrix_postsvd]
Ci_h_matrix_postsvd_buf = Ci_h_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_h_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_h_matrix_postsvd')
stop
else:
# !!!
kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
#indcrep = kp + (k-1)*n_svd + (lp-1)*n_svd**2 + (l-1)*n_svd**3
#file.write( '{:5} {:5} {:5} {:5} {:5} {:5} \n'.format(indc, indc-indcrep, kp, k, lp, l ) )
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_h_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_h_matrix_postsvd[indc-1] = float( line[2] )
# !!!
#Ci_h_matrix_postsvd = np.reshape(Ci_h_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
#file.close()
return(Ci_h_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Ci_overlap_matrix_postsvd():
# !!!
Ci_overlap_matrix_postsvd = np.zeros( (n_svd*n_svd , n_svd*n_svd) )
# !!!
beg_Ci_overlap_matrix_postsvd = results.find('Ci_overlap_matrix_postsvd : [ ') + len( 'Ci_overlap_matrix_postsvd : [ ' )
end_Ci_overlap_matrix_postsvd = len(results)
Ci_overlap_matrix_postsvd_buf = results[beg_Ci_overlap_matrix_postsvd:end_Ci_overlap_matrix_postsvd]
Ci_overlap_matrix_postsvd_buf = Ci_overlap_matrix_postsvd_buf.split( '\n' )
# !!!
for iline in range(1, n_svd**4+1):
# !!!
line = Ci_overlap_matrix_postsvd_buf[iline].split()
indc = int( line[0] )
errS = float( line[4] )
#if( errS>eps ):
#print( line )
if( indc != iline ):
print('Error in reading Ci_overlap_matrix_postsvd')
stop
else:
# !!!
#kp = indc % n_svd
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
indc2 = int( ( indc1 - (k-1) ) / n_svd )
lp = indc2 % n_svd + 1
l = int( ( indc2 - (lp-1) ) / n_svd ) + 1
# !!!
irow = kp + (k-1)*n_svd - 1
icol = lp + (l-1)*n_svd - 1
Ci_overlap_matrix_postsvd[irow][icol] = float( line[2] )
#Ci_overlap_matrix_postsvd[indc-1] = float( line[2] )
# !!!
# !!!
#Ci_overlap_matrix_postsvd = np.reshape(Ci_overlap_matrix_postsvd, (n_svd*n_svd, n_svd*n_svd), order='F')
# !!!
return(Ci_overlap_matrix_postsvd)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def check_symmetric(a, tol=1e-3):
return np.all(np.abs(a-a.T) < tol)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def save_results_to_resultsQMC():
file = open('resultsQMC.txt','a')
file.write('\n \n \n')
file.write('- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n')
file.write("Today's date: {}\n".format(datetime.now()))
file.write("EZFIO file = {}\n".format(EZFIO_file))
file.write('\n')
file.write( results )
file.write('\n')
file.write('+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\n \n')
file.close()
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Esvd():
# !!!
# read CI_SVD matrices
Ci_h_matrix_svd = get_Ci_h_matrix_svd()
Ci_overlap_matrix_svd = get_Ci_overlap_matrix_svd()
#print( 'Ci_h_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_svd)) )
#print( 'Ci_overlap_matrix_svd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_svd)) )
# !!!
# symmetrise and diagonalise
aa = Ci_h_matrix_svd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_svd
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
#print( eigvals_svd + E_toadd )
recouvre_svd = np.abs(psi_svd_coeff @ vr)
ind_gssvd = np.argmax(recouvre_svd)
# !!!
E_svd = eigvals_svd[ind_gssvd] + E_toadd
return( E_svd, vr[:,ind_gssvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Epostsvd():
# !!!
# read CI_postSVD matrices
Ci_h_matrix_postsvd = get_Ci_h_matrix_postsvd()
Ci_overlap_matrix_postsvd = get_Ci_overlap_matrix_postsvd()
#print( 'Ci_h_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_h_matrix_postsvd)) )
#print( 'Ci_overlap_matrix_postsvd is symmetric ? {}' .format(check_symmetric(Ci_overlap_matrix_postsvd)) )
# !!!
# symmetrise and diagonalise
aa = Ci_h_matrix_postsvd
aa = 0.5*( aa + aa.T )
bb = Ci_overlap_matrix_postsvd
eigvals_postsvd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
#print( eigvals_postsvd + E_toadd )
d_postsvd = np.diagflat(psi_svd_coeff)
d_postsvd = d_postsvd.reshape( (1,n_svd*n_svd) )
recouvre_postsvd = np.abs(d_postsvd @ vr)
ind_gspostsvd = np.argmax(recouvre_postsvd)
#print(recouvre_postsvd, ind_gspostsvd)
# !!!
#print( eigvals_postsvd.shape )
E_postsvd = eigvals_postsvd[ind_gspostsvd] + E_toadd
# !!!
return( E_postsvd, vr[:,ind_gspostsvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def SVD_postsvd(sigma_postsvd):
# !!!
print( 'performing new SVD for the post SVD eigenvector:' )
# !!!
#sigma_postsvd = sigma_postsvd.reshape( (n_svd,n_svd) )
#sigma_postsvd = sigma_postsvd.reshape( n_svd, n_svd, order='F' )
#print( 'sigma_postsvd is symmetric ? {}' .format(check_symmetric(sigma_postsvd)) )
# !!!
sigma_postsvd_mat = np.zeros( (n_svd,n_svd) )
for indc in range(1, n_svd**2+1):
if( ( indc % n_svd ) !=0 ):
kp = indc % n_svd
else:
kp = n_svd
indc1 = int( ( indc - kp ) / n_svd )
k = indc1 % n_svd + 1
irow = kp + (k-1)*n_svd - 1
sigma_postsvd_mat[kp-1][k-1] = sigma_postsvd[irow]
sigma_postsvd = sigma_postsvd_mat
# !!!
# construct the new matrix Y
Y = U_svd @ sigma_postsvd @ V_svd.T
normY = np.linalg.norm(Y, ord='fro')
# !!!
# parameters of RSVD
rank = n_svd
npow = 10
nb_oversamp = 10
# !!!
# call RSV
U_postSVD, sigma_postsvd_diag, VT_postsvd = powit_RSVD(Y, rank, npow, nb_oversamp)
# !!!
# check precision
Y_SVD = np.dot( U_postSVD , np.dot( np.diag(sigma_postsvd_diag) , VT_postsvd ) )
energy = np.sum( np.square(sigma_postsvd_diag) ) / normY**2
err_SVD = 100. * np.linalg.norm( Y - Y_SVD, ord="fro") / normY
print('energy = {}, error = {}\n'.format(energy, err_SVD))
# !!!
return(U_postSVD, sigma_postsvd_diag, VT_postsvd)
# !!!
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Hsvd_QP(Hsvd_qp_txt):
Hsvd_qp = np.zeros( (n_svd,n_svd) )
Hsvd_qp_file = open(Hsvd_qp_txt, 'r')
for line in Hsvd_qp_file:
line = line.split()
i = int(line[0]) - 1
j = int(line[1]) - 1
Hsvd_qp[i,j] = float(line[2])
return(Hsvd_qp)
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
def get_Esvd_QP(Hsvd_qp):
# !!!
# symmetrise and diagonalise
aa = Hsvd_qp
aa = 0.5*( aa + aa.T )
bb = np.identity(n_svd)
eigvals_svd, vr = eig(aa, bb, left=False, right=True, overwrite_a=True, overwrite_b=True,
check_finite=True, homogeneous_eigvals=False)
recouvre_svd = np.abs(psi_svd_coeff @ vr)
ind_gssvd = np.argmax(recouvre_svd)
E_svd = eigvals_svd[ind_gssvd] + E_toadd
return( E_svd, vr[:,ind_gssvd] )
# ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ ! ~ !
if __name__ == '__main__':
t0 = time.time()
# !!!
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
EZFIO_file = "/home/aammar/qp2/src/svdwf/h2o_631g_J_art"
E_toadd = 9.194966082434476 #6.983610961797779
# ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ #
# !!!
ezfio.set_file(EZFIO_file)
n_svd = ezfio.get_spindeterminants_n_svd_coefs()
psi_svd_coeff = np.array(ezfio.get_spindeterminants_psi_svd_coefs())
U_svd = np.array(ezfio.get_spindeterminants_psi_svd_alpha())
V_svd = np.array(ezfio.get_spindeterminants_psi_svd_beta())
# !!!
#print( U_svd.shape )
U_svd = U_svd[0,:,:].T
#print( U_svd.shape )
V_svd = V_svd[0,:,:].T
# !!!
print("Today's date:", datetime.now() )
print("EZFIO file = {}".format(EZFIO_file))
print("nuclear energy = {}".format(E_toadd) )
print("n_svd = {} \n".format(n_svd) )
# !!!
#set_vmc_params()
#run_qmc()
#print("start QMC:")
#stop_qmc()
# !!!
print( 'getting QMCCHEM results from {}'.format(EZFIO_file) )
results = subprocess.check_output(['qmcchem', 'result', EZFIO_file], encoding='UTF-8')
# !!!
Eloc, ErrEloc = get_energy()
print('Eloc = {} +/- {}'.format(Eloc, ErrEloc))
print('{} <= Eloc <= {}\n'.format(Eloc-ErrEloc,Eloc+ErrEloc))
# !!!
save_resultsQMC = input( 'save QMC results from {}? (y/n) '.format(EZFIO_file) )
if( save_resultsQMC == 'y' ):
print('saving in resultsQMC.txt')
save_results_to_resultsQMC()
print('\n')
# !!!
read_QPsvd = input( 'read QP Hsvd matrix ? (y/n) ')
if( read_QPsvd == 'y' ):
Hsvd_qp_txt = input('name of file with QM H_svd matrix:')
Hsvd_qp = get_Hsvd_QP(Hsvd_qp_txt)
E_svd_QP, sigma_svd_QP = get_Esvd_QP(Hsvd_qp)
print('QP SVD enegry = {} \n'.format(E_svd_QP) )
print('\n')
# !!!
E_svd, sigma_svd = get_Esvd()
print('svd enegry = {} \n '.format(E_svd) )
# !!!
E_postsvd, sigma_postsvd = get_Epostsvd()
print('post svd energy = {} \n'.format(E_postsvd) )
# !!!
save_to_EZFIO = input( "modify EZFIO (with svd_QP, svd_QMC or postsvd)? " )
# !!!
if( save_to_EZFIO == 'svd_QMC' ):
ezfio.set_spindeterminants_psi_svd_coefs( sigma_svd )
direc_svdcoeff = EZFIO_file + '/spindeterminants/psi_svd_coefs.gz'
print( '{} is modified'.format(direc_svdcoeff) )
print( 'precedent svd coeff:' )
print(psi_svd_coeff)
print( 'current svd coeff:' )
print(sigma_svd)
# !!!
elif( save_to_EZFIO == 'svd_QP'):
ezfio.set_spindeterminants_psi_svd_coefs( sigma_svd_QP )
direc_svdcoeff = EZFIO_file + '/spindeterminants/psi_svd_coefs.gz'
print( '{} is modified'.format(direc_svdcoeff) )
print( 'precedent svd coeff:' )
print(psi_svd_coeff)
print( 'current svd coeff:' )
print(sigma_svd_QP)
# !!!
elif( save_to_EZFIO == 'postsvd' ):
# SVD first
U_postSVD, sigma_postsvd_diag, V_postSVD = SVD_postsvd(sigma_postsvd)
V_postSVD = V_postSVD.T
# save next in ezfio file
U_postSVD_toEZFIO = np.zeros( ( U_postSVD.shape[0], U_postSVD.shape[1], 1) )
V_postSVD_toEZFIO = np.zeros( ( V_postSVD.shape[0], V_postSVD.shape[1], 1) )
U_postSVD_toEZFIO[:,:,0] = U_postSVD
V_postSVD_toEZFIO[:,:,0] = V_postSVD
#
ezfio.set_spindeterminants_psi_svd_alpha( U_postSVD_toEZFIO )
ezfio.set_spindeterminants_psi_svd_coefs( sigma_postsvd_diag )
ezfio.set_spindeterminants_psi_svd_beta( V_postSVD_toEZFIO )
# !!!
else:
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
exit()
# !!!
print("end after {:.3f} minutes".format((time.time()-t0)/60.) )
# !!!
# !!!

10
src/test_SVD/h2o/QR.py Normal file
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# !!!
import numpy as np
# !!!
def QR_fact(X):
Q, R = np.linalg.qr(X, mode="reduced")
D = np.diag( np.sign( np.diag(R) ) )
Qunique = np.dot(Q,D)
#Runique = np.dot(D,R)
return(Qunique)
# !!!

20
src/test_SVD/h2o/RSVD.py Normal file
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# !!!
import numpy as np
from QR import QR_fact
# !!!
def powit_RSVD(X, new_r, nb_powit, nb_oversamp):
# !!!
G = np.random.randn(X.shape[1], new_r+nb_oversamp)
Q = QR_fact( np.dot(X,G) )
# !!!
for _ in range(nb_powit):
Q = QR_fact( np.dot(X.T,Q) )
Q = QR_fact( np.dot(X,Q) )
# !!!
Y = np.dot(Q.T,X)
# !!!
U, S, VT = np.linalg.svd(Y, full_matrices=0)
U = np.dot(Q,U)
return U[:,:(new_r)], S[:(new_r)], VT[:(new_r),:]
# !!!
# !!!