Merge branch 'QuantumPackage-dev-stable' into dev-stable-tc-scf

config/ifort_2021_xHost.cfg

@@ -6,7 +6,7 @@
 # --align=32                 : Align all provided arrays on a 32-byte boundary
 #
 [COMMON]
-FC           : ifort -fpic
+FC           : ifort -fpic -diag-disable 5462
 LAPACK_LIB   : -mkl=parallel
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=64 -DINTEL 

configure

@@ -232,7 +232,7 @@ EOF
 
             execute << EOF
               cd "\${QP_ROOT}"/external
-              tar --gunzip --extract --file qp2-dependencies/f77-zmq-4.3.2.tar.gz
+              tar --gunzip --extract --file qp2-dependencies/f77-zmq-4.3.?.tar.gz
               cd f77-zmq-*
               ./configure --prefix=\$QP_ROOT
               export ZMQ_H="\$QP_ROOT"/include/zmq.h

scripts/compilation/qp_create_ninja

@@ -25,7 +25,7 @@ except ImportError:
                                       "quantum_package.rc"))
 
     print("\n".join(["", "Error:", "source %s" % f, ""]))
-    sys.exit(1)
+    raise
 
 # Compress path
 def comp_path(path):

scripts/qp_exc_energy.py

@@ -0,0 +1,186 @@
+#!/usr/bin/env python
+# Computes the error on the excitation energy of a CIPSI run.
+
+def student(p,df):
+    import scipy
+    from scipy.stats import t
+    return t.ppf(p, df)
+
+
+def chi2cdf(x,k):
+    import scipy
+    import scipy.stats
+    return scipy.stats.chi2.cdf(x,k)
+
+
+def jarque_bera(data):
+
+    n    = max(len(data), 2)
+    norm = 1./ sum( [ w for (_,w) in data ] )
+
+    mu     =   sum( [ w* x        for (x,w) in data ] ) * norm
+    sigma2 =   sum( [ w*(x-mu)**2 for (x,w) in data ] ) * norm
+    if sigma2 > 0.:
+      S      = ( sum( [ w*(x-mu)**3 for (x,w) in data ] ) * norm ) / sigma2**(3./2.)
+      K      = ( sum( [ w*(x-mu)**4 for (x,w) in data ] ) * norm ) / sigma2**2
+    else:
+      S = 0.
+      K = 0.
+
+    # Value of the Jarque-Bera test
+    JB = n/6. * (S**2 + 1./4. * (K-3.)**2)
+
+    # Probability that the data comes from a Gaussian distribution
+    p = 1. - chi2cdf(JB,2)
+
+    return JB, mu, sqrt(sigma2/(n-1)), p
+
+
+
+to_eV = 27.2107362681
+import sys, os
+import scipy
+import scipy.stats
+from math import sqrt, gamma, exp
+import json
+
+
+def read_data(filename,state):
+  """ Read energies and PT2 from input file """
+  with open(filename,'r') as f:
+      lines = json.load(f)['fci']
+
+  print(f"State: {state}")
+
+  gs = []
+  es = []
+
+  for l in lines:
+      try:
+        pt2_0 = l['states'][0]['pt2']
+        e_0   = l['states'][0]['energy']
+        pt2_1 = l['states'][state]['pt2']
+        e_1   = l['states'][state]['energy']
+        gs.append( (e_0, pt2_0) )
+        es.append( (e_1, pt2_1) )
+      except: pass
+
+  def f(p_1, p0, p1):
+      e, pt2 = p0
+      y0, x0 = p_1
+      y1, x1 = p1
+      try:
+        alpha = (y1-y0)/(x0-x1)
+      except ZeroDivisionError:
+        alpha = 1.
+      return [e, pt2, alpha]
+
+  for l in (gs, es):
+      p_1, p0, p1 = l[0], l[0], l[1]
+      l[0] = f(p_1, p0, p1)
+
+      for i in range(1,len(l)-1):
+          p_1 = (l[i-1][0], l[i-1][1])
+          p0  = l[i]
+          p1  = l[i+1]
+          l[i] = f(p_1, p0, p1)
+
+      i = len(l)-1
+      p_1 = (l[i-1][0], l[i-1][1])
+      p0  = l[i]
+      p1  = l[-1]
+      l[i] = f(p_1, p0, p1)
+
+  return [ x+y for x,y in zip(gs,es) ]
+
+
+def compute(data):
+
+    d = []
+    for e0, p0, a0, e1, p1, a1 in data:
+        x   = (e1+p1)-(e0+p0)
+        w   = 1./sqrt(p0**2 + p1**2)
+        bias = (a1-1.)*p1 - (a0-1.)*p0
+        d.append( (x,w,bias) )
+
+    x = []
+    target = (scipy.stats.norm.cdf(1.)-0.5)*2   # = 0.6827
+
+    print("| %2s | %8s | %8s | %8s | %8s | %8s |"%( "N", "DE", "+/-", "bias", "P(G)", "J"))
+    print("|----+----------+----------+----------+----------+----------|")
+    xmax = (0.,0.,0.,0.,0.,0,0.)
+    for i in range(len(data)-1):
+        jb, mu, sigma, p = jarque_bera( [ (x,w) for (x,w,bias) in d[i:] ] )
+        bias = sum ( [ w * e for (_,w,e) in d[i:] ] ) / sum ( [ w for (_,w,_) in d[i:] ] )
+        mu = (mu+0.5*bias) * to_eV
+        sigma = sigma * to_eV
+        bias = bias * to_eV
+        n = len(data[i:])
+        beta = student(0.5*(1.+target/p) ,n)
+        err = sigma * beta + 0.5*abs(bias)
+        print("| %2d | %8.3f | %8.3f | %8.3f | %8.3f | %8.3f |"%( n, mu, err, bias, p, jb))
+        if n < 3 :
+            continue
+        y = (err, p, mu, err, jb,n,bias)
+        if p > xmax[1]: xmax = y
+        if p < 0.8:
+            continue
+        x.append(y)
+
+    x = sorted(x)
+
+    print("|----+----------+----------+----------+----------+----------|")
+    if x != []:
+      xmax = x[0]
+    _, p, mu, err, jb, n, bias = xmax
+    beta = student(0.5*(1.+target/p),n)
+    print("| %2d | %8.3f | %8.3f | %8.3f | %8.3f | %8.3f |\n"%(n, mu, err, bias, p, jb))
+
+    return mu, err, bias, p
+
+filename = sys.argv[1]
+print(filename)
+if len(sys.argv) > 2:
+    state = int(sys.argv[2])
+else:
+    state = 1
+data = read_data(filename,state)
+mu, err, bias, _ = compute(data)
+print(" %s: %8.3f +/- %5.3f eV\n"%(filename, mu, err))
+
+import numpy as np
+A = np.array( [ [ data[-1][1], 1. ],
+                [ data[-2][1], 1. ] ] )
+B = np.array( [ [ data[-1][0] ],
+                [ data[-2][0] ] ] )
+E0 = np.linalg.solve(A,B)[1]
+A = np.array( [ [ data[-1][4], 1. ],
+                [ data[-2][4], 1. ] ] )
+B = np.array( [ [ data[-1][3] ],
+                [ data[-2][3] ] ] )
+E1 = np.linalg.solve(A,B)[1]
+average_2 = (E1-E0)*to_eV
+
+A = np.array( [ [ data[-1][1], 1. ],
+                [ data[-2][1], 1. ],
+                [ data[-3][1], 1. ] ] )
+B = np.array( [ [ data[-1][0] ],
+                [ data[-2][0] ],
+                [ data[-3][0] ] ] )
+E0 = np.linalg.lstsq(A,B,rcond=None)[0][1]
+A = np.array( [ [ data[-1][4], 1. ],
+                [ data[-2][4], 1. ],
+                [ data[-3][4], 1. ] ] )
+B = np.array( [ [ data[-1][3] ],
+                [ data[-2][3] ],
+                [ data[-3][3] ] ] )
+E1 = np.linalg.lstsq(A,B,rcond=None)[0][1]
+average_3 = (E1-E0)*to_eV
+
+exc = ((data[-1][3] + data[-1][4]) - (data[-1][0] + data[-1][1])) * to_eV
+error_2 = abs(average_2 - average_3)
+error_3 = abs(average_3 - exc)
+print(" 2-3 points: %.3f +/- %.3f "% (average_3, error_2))
+print(" largest wf: %.3f +/- %.3f  "%(average_3, error_3))
+
+

src/ao_two_e_ints/EZFIO.cfg

@@ -18,3 +18,8 @@ interface: ezfio,provider,ocaml
 default: False
 ezfio_name: direct
 
+[do_ao_cholesky]
+type: logical
+doc: Perform Cholesky decomposition of AO integrals
+interface: ezfio,provider,ocaml
+default: True

src/ao_two_e_ints/cholesky.irp.f

@@ -0,0 +1,100 @@
+BEGIN_PROVIDER [ integer, cholesky_ao_num_guess ]
+ implicit none
+ BEGIN_DOC
+ ! Number of Cholesky vectors in AO basis
+ END_DOC
+
+ integer :: i,j,k,l
+ double precision :: xnorm0, x, integral
+ double precision, external :: ao_two_e_integral
+
+ cholesky_ao_num_guess = 0
+ xnorm0 = 0.d0
+ x = 0.d0
+ do j=1,ao_num
+   do i=1,ao_num
+     integral = ao_two_e_integral(i,i,j,j)
+     if (integral > ao_integrals_threshold) then
+       cholesky_ao_num_guess += 1
+     else
+       x += integral
+     endif
+   enddo
+ enddo
+ print *, 'Cholesky decomposition of AO integrals'
+ print *, '--------------------------------------'
+ print *, ''
+ print *, 'Estimated Error: ', x
+ print *, 'Guess size: ', cholesky_ao_num_guess, '(', 100.d0*dble(cholesky_ao_num_guess)/dble(ao_num*ao_num), ' %)'
+
+END_PROVIDER
+
+ BEGIN_PROVIDER [ integer, cholesky_ao_num ]
+&BEGIN_PROVIDER [ double precision, cholesky_ao, (ao_num, ao_num, cholesky_ao_num_guess) ]
+ use mmap_module
+ implicit none
+ BEGIN_DOC
+ ! Cholesky vectors in AO basis: (ik|a):
+ ! <ij|kl> = (ik|jl) = sum_a (ik|a).(a|jl)
+ END_DOC
+
+ type(c_ptr) :: ptr
+ integer :: fd, i,j,k,l, rank
+ double precision, pointer :: ao_integrals(:,:,:,:)
+ double precision, external :: ao_two_e_integral
+
+ ! Store AO integrals in a memory mapped file
+ call mmap(trim(ezfio_work_dir)//'ao_integrals', &
+   (/ int(ao_num,8), int(ao_num,8), int(ao_num,8), int(ao_num,8) /), &
+   8, fd, .False., ptr)
+ call c_f_pointer(ptr, ao_integrals, (/ao_num, ao_num, ao_num, ao_num/))
+
+ double precision :: integral
+ logical, external :: ao_two_e_integral_zero
+ !$OMP PARALLEL DO DEFAULT(SHARED) PRIVATE(i,j,k,l, integral) SCHEDULE(dynamic)
+ do l=1,ao_num
+  do j=1,l
+   do k=1,ao_num
+    do i=1,k
+     if (ao_two_e_integral_zero(i,j,k,l)) cycle
+     integral = ao_two_e_integral(i,k,j,l)
+     ao_integrals(i,k,j,l) = integral
+     ao_integrals(k,i,j,l) = integral
+     ao_integrals(i,k,l,j) = integral
+     ao_integrals(k,i,l,j) = integral
+    enddo
+   enddo
+  enddo
+ enddo
+ !$OMP END PARALLEL DO
+
+ ! Call Lapack
+ cholesky_ao_num = cholesky_ao_num_guess
+ call pivoted_cholesky(ao_integrals, cholesky_ao_num, ao_integrals_threshold, ao_num*ao_num, cholesky_ao)
+ print *, 'Rank: ', cholesky_ao_num, '(', 100.d0*dble(cholesky_ao_num)/dble(ao_num*ao_num), ' %)'
+
+ ! Remove mmap
+ double precision, external :: getUnitAndOpen
+ call munmap( &
+   (/ int(ao_num,8), int(ao_num,8), int(ao_num,8), int(ao_num,8) /), &
+   8, fd, ptr)
+ open(unit=99,file=trim(ezfio_work_dir)//'ao_integrals')
+ close(99, status='delete')
+
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, cholesky_ao_transp, (cholesky_ao_num, ao_num, ao_num) ]
+ implicit none
+ BEGIN_DOC
+! Transposed of the Cholesky vectors in AO basis set
+ END_DOC
+ integer :: i,j,k
+ do j=1,ao_num
+  do i=1,ao_num
+   do k=1,ao_num
+    cholesky_ao_transp(k,i,j) = cholesky_ao(i,j,k)
+   enddo
+  enddo
+ enddo
+END_PROVIDER
+

src/ao_two_e_ints/map_integrals.irp.f

@@ -486,7 +486,7 @@ subroutine get_ao_two_e_integrals(j,k,l,sze,out_val)
   PROVIDE ao_two_e_integrals_in_map ao_integrals_map
 
   if (ao_one_e_integral_zero(j,l)) then
-    out_val = 0.d0
+    out_val(1:sze) = 0.d0
     return
   endif
 

src/cipsi/NEED

@@ -1,3 +1,4 @@
+json
 perturbation
 zmq
 mpi

src/cipsi/cipsi.irp.f

@@ -16,7 +16,6 @@ subroutine run_cipsi
   double precision, external :: memory_of_double
   PROVIDE H_apply_buffer_allocated
 
-  N_iter = 1
   threshold_generators = 1.d0
   SOFT_TOUCH threshold_generators
 
@@ -76,7 +75,6 @@ subroutine run_cipsi
         )
       write(*,'(A)')  '--------------------------------------------------------------------------------'
 
-
     to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor)
     to_select = max(N_states_diag, to_select)
     if (do_pt2) then
@@ -106,10 +104,10 @@ subroutine run_cipsi
 
     call save_energy(psi_energy_with_nucl_rep, pt2_data % pt2)
 
-    call save_iterations(psi_energy_with_nucl_rep(1:N_states),pt2_data % rpt2,N_det)
+    call increment_n_iter(psi_energy_with_nucl_rep, pt2_data)
     call print_extrapolated_energy()
     call print_mol_properties()
-    N_iter += 1
+    call write_cipsi_json(pt2_data,pt2_data_err)
 
     if (qp_stop()) exit
 
@@ -130,13 +128,13 @@ subroutine run_cipsi
     if (qp_stop()) exit
   enddo
 
-  if (.not.qp_stop()) then
+  ! If stopped because N_det > N_det_max, do an extra iteration to compute the PT2
-    if (N_det < N_det_max) then
+  if ((.not.qp_stop()).and.                                          &
-        call diagonalize_CI
+        (N_det > N_det_max) .and.                                    &
-        call save_wavefunction
+        (maxval(abs(pt2_data % pt2(1:N_states))) > pt2_max) .and.    &
-        call save_energy(psi_energy_with_nucl_rep, zeros)
+        (maxval(abs(pt2_data % variance(1:N_states))) > variance_max) .and.&
-    endif
+        (correlation_energy_ratio <= correlation_energy_ratio_max)   &
-
+        ) then
     if (do_pt2) then
       call pt2_dealloc(pt2_data)
       call pt2_dealloc(pt2_data_err)
@@ -155,11 +153,13 @@ subroutine run_cipsi
     call save_energy(psi_energy_with_nucl_rep, pt2_data % pt2)
     call print_summary(psi_energy_with_nucl_rep(1:N_states), &
       pt2_data, pt2_data_err, N_det,N_configuration,N_states,psi_s2)
-    call save_iterations(psi_energy_with_nucl_rep(1:N_states),pt2_data % rpt2,N_det)
+    call increment_n_iter(psi_energy_with_nucl_rep, pt2_data)
     call print_extrapolated_energy()
     call print_mol_properties()
+    call write_cipsi_json(pt2_data,pt2_data_err)
   endif
   call pt2_dealloc(pt2_data)
   call pt2_dealloc(pt2_data_err)
 
 end
+

src/cipsi/environment.irp.f

@@ -7,7 +7,9 @@ BEGIN_PROVIDER [ integer, nthreads_pt2 ]
  character*(32) :: env
  call getenv('QP_NTHREADS_PT2',env)
  if (trim(env) /= '') then
+   call lock_io()
    read(env,*) nthreads_pt2
+   call unlock_io()
    call write_int(6,nthreads_pt2,'Target number of threads for PT2')
  endif
 END_PROVIDER

src/cipsi/stochastic_cipsi.irp.f

@@ -15,7 +15,6 @@ subroutine run_stochastic_cipsi
   double precision, external :: memory_of_double
   PROVIDE H_apply_buffer_allocated distributed_davidson mo_two_e_integrals_in_map
 
-  N_iter = 1
   threshold_generators = 1.d0
   SOFT_TOUCH threshold_generators
 
@@ -96,10 +95,10 @@ subroutine run_stochastic_cipsi
 
     call save_energy(psi_energy_with_nucl_rep, pt2_data % pt2)
 
-    call save_iterations(psi_energy_with_nucl_rep(1:N_states),pt2_data % rpt2,N_det)
+    call increment_n_iter(psi_energy_with_nucl_rep, pt2_data)
     call print_extrapolated_energy()
     call print_mol_properties()
-    N_iter += 1
+    call write_cipsi_json(pt2_data,pt2_data_err)
 
     if (qp_stop()) exit
 
@@ -119,13 +118,13 @@ subroutine run_stochastic_cipsi
     if (qp_stop()) exit
   enddo
 
-  if (.not.qp_stop()) then
+  ! If stopped because N_det > N_det_max, do an extra iteration to compute the PT2
-    if (N_det < N_det_max) then
+  if ((.not.qp_stop()).and.                                          &
-        call diagonalize_CI
+        (N_det > N_det_max) .and.                                    &
-        call save_wavefunction
+        (maxval(abs(pt2_data % pt2(1:N_states))) > pt2_max) .and.    &
-        call save_energy(psi_energy_with_nucl_rep, zeros)
+        (maxval(abs(pt2_data % variance(1:N_states))) > variance_max) .and.&
-    endif
+        (correlation_energy_ratio <= correlation_energy_ratio_max)   &
-
+        ) then
     call pt2_dealloc(pt2_data)
     call pt2_dealloc(pt2_data_err)
     call pt2_alloc(pt2_data, N_states)
@@ -135,9 +134,10 @@ subroutine run_stochastic_cipsi
     call save_energy(psi_energy_with_nucl_rep, pt2_data % pt2)
     call print_summary(psi_energy_with_nucl_rep, &
        pt2_data , pt2_data_err, N_det, N_configuration, N_states, psi_s2)
-    call save_iterations(psi_energy_with_nucl_rep(1:N_states),pt2_data % rpt2,N_det)
+    call increment_n_iter(psi_energy_with_nucl_rep, pt2_data)
     call print_extrapolated_energy()
     call print_mol_properties()
+    call write_cipsi_json(pt2_data,pt2_data_err)
   endif
   call pt2_dealloc(pt2_data)
   call pt2_dealloc(pt2_data_err)

src/cipsi/write_cipsi_json.irp.f

@@ -0,0 +1,53 @@
+subroutine write_cipsi_json(pt2_data, pt2_data_err)
+    use selection_types
+    implicit none
+    BEGIN_DOC
+!  Writes JSON data for CIPSI runs
+    END_DOC
+    type(pt2_type), intent(in) :: pt2_data, pt2_data_err
+    integer :: i,j,k
+
+    call lock_io
+    character*(64), allocatable    :: fmtk(:)
+    integer :: N_states_p, N_iter_p
+    N_states_p = min(N_states,N_det)
+    N_iter_p = min(N_iter,8)
+    allocate(fmtk(0:N_iter_p))
+    fmtk(:) = '(''   '',E22.15,'','')'
+    fmtk(N_iter_p) = '(''   '',E22.15)'
+
+    write(json_unit, json_dict_uopen_fmt)
+    write(json_unit, json_int_fmt) 'n_det', N_det
+    if (s2_eig) then
+      write(json_unit, json_int_fmt) 'n_cfg', N_configuration
+      if (only_expected_s2) then
+        write(json_unit, json_int_fmt) 'n_csf', N_csf
+      endif
+    endif
+    write(json_unit, json_array_open_fmt) 'states'
+    do k=1,N_states_p
+      write(json_unit, json_dict_uopen_fmt)
+      write(json_unit, json_real_fmt) 'energy', psi_energy_with_nucl_rep(k)
+      write(json_unit, json_real_fmt) 's2', psi_s2(k)
+      write(json_unit, json_real_fmt) 'pt2', pt2_data % pt2(k)
+      write(json_unit, json_real_fmt) 'pt2_err', pt2_data_err % pt2(k)
+      write(json_unit, json_real_fmt) 'rpt2', pt2_data % rpt2(k)
+      write(json_unit, json_real_fmt) 'rpt2_err', pt2_data_err % rpt2(k)
+      write(json_unit, json_real_fmt) 'variance', pt2_data % variance(k)
+      write(json_unit, json_real_fmt) 'variance_err', pt2_data_err % variance(k)
+      write(json_unit, json_array_open_fmt) 'ex_energy'
+      do i=2,N_iter_p
+          write(json_unit, fmtk(i)) extrapolated_energy(i,k)
+      enddo
+      write(json_unit, json_array_close_fmtx)
+      if (k < N_states_p) then
+        write(json_unit, json_dict_close_fmt)
+      else
+        write(json_unit, json_dict_close_fmtx)
+      endif
+    enddo
+    write(json_unit, json_array_close_fmtx)
+    write(json_unit, json_dict_close_fmt)
+    deallocate(fmtk)
+    call unlock_io
+end

src/cipsi_tc_bi_ortho/NEED

@@ -1,6 +1,7 @@
+json
 mpi
 perturbation
 zmq
-iterations_tc
+iterations
 csf
 tc_bi_ortho

src/cipsi_tc_bi_ortho/stochastic_cipsi.irp.f

@@ -94,7 +94,15 @@ subroutine run_stochastic_cipsi
     call ZMQ_pt2(E_denom, pt2_data, pt2_data_err, relative_error,to_select) ! Stochastic PT2 and selection
 !    stop
 
-    N_iter += 1
+    call print_summary(psi_energy_with_nucl_rep, &
+       pt2_data, pt2_data_err, N_det,N_configuration,N_states,psi_s2)
+
+    call save_energy(psi_energy_with_nucl_rep, pt2_data % pt2)
+
+    call increment_n_iter(psi_energy_with_nucl_rep, pt2_data)
+    call print_extrapolated_energy()
+!    call print_mol_properties()
+    call write_cipsi_json(pt2_data,pt2_data_err)
 
     if (qp_stop()) exit
 

src/cipsi_tc_bi_ortho/write_cipsi_json.irp.f

@@ -0,0 +1,53 @@
+subroutine write_cipsi_json(pt2_data, pt2_data_err)
+    use selection_types
+    implicit none
+    BEGIN_DOC
+!  Writes JSON data for CIPSI runs
+    END_DOC
+    type(pt2_type), intent(in) :: pt2_data, pt2_data_err
+    integer :: i,j,k
+
+    call lock_io
+    character*(64), allocatable    :: fmtk(:)
+    integer :: N_states_p, N_iter_p
+    N_states_p = min(N_states,N_det)
+    N_iter_p = min(N_iter,8)
+    allocate(fmtk(0:N_iter_p))
+    fmtk(:) = '(''   '',E22.15,'','')'
+    fmtk(N_iter_p) = '(''   '',E22.15)'
+
+    write(json_unit, json_dict_uopen_fmt)
+    write(json_unit, json_int_fmt) 'n_det', N_det
+    if (s2_eig) then
+      write(json_unit, json_int_fmt) 'n_cfg', N_configuration
+      if (only_expected_s2) then
+        write(json_unit, json_int_fmt) 'n_csf', N_csf
+      endif
+    endif
+    write(json_unit, json_array_open_fmt) 'states'
+    do k=1,N_states_p
+      write(json_unit, json_dict_uopen_fmt)
+      write(json_unit, json_real_fmt) 'energy', psi_energy_with_nucl_rep(k)
+      write(json_unit, json_real_fmt) 's2', psi_s2(k)
+      write(json_unit, json_real_fmt) 'pt2', pt2_data % pt2(k)
+      write(json_unit, json_real_fmt) 'pt2_err', pt2_data_err % pt2(k)
+      write(json_unit, json_real_fmt) 'rpt2', pt2_data % rpt2(k)
+      write(json_unit, json_real_fmt) 'rpt2_err', pt2_data_err % rpt2(k)
+      write(json_unit, json_real_fmt) 'variance', pt2_data % variance(k)
+      write(json_unit, json_real_fmt) 'variance_err', pt2_data_err % variance(k)
+      write(json_unit, json_array_open_fmt) 'ex_energy'
+      do i=2,N_iter_p
+          write(json_unit, fmtk(i)) extrapolated_energy(i,k)
+      enddo
+      write(json_unit, json_array_close_fmtx)
+      if (k < N_states_p) then
+        write(json_unit, json_dict_close_fmt)
+      else
+        write(json_unit, json_dict_close_fmtx)
+      endif
+    enddo
+    write(json_unit, json_array_close_fmtx)
+    write(json_unit, json_dict_close_fmt)
+    deallocate(fmtk)
+    call unlock_io
+end

src/davidson/davidson_parallel.irp.f

@@ -150,7 +150,9 @@ subroutine davidson_slave_work(zmq_to_qp_run_socket, zmq_socket_push, N_st, sze,
       exit
     endif
     if(task_id == 0) exit
+    call lock_io()
     read (msg,*) imin, imax, ishift, istep
+    call unlock_io()
     integer :: k
     do k=imin,imax
       v_t(:,k) = 0.d0
@@ -546,6 +548,8 @@ end
 
 
 
+
+
 integer function zmq_put_N_states_diag(zmq_to_qp_run_socket,worker_id)
   use f77_zmq
   implicit none

src/davidson/diagonalization_hs2_dressed.irp.f

@@ -461,9 +461,8 @@ subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_
        integer :: lwork, info
        double precision, allocatable :: work(:)
 
-
        y = h
-       !y = h_p
+!       y = h_p   ! Doesn't work for non-singlets
        lwork = -1
        allocate(work(1))
        call dsygv(1,'V','U',shift2,y,size(y,1), &

src/ezfio_files/lock.irp.f

@@ -9,4 +9,21 @@ BEGIN_PROVIDER [ integer(omp_lock_kind), file_lock ]
   call omp_init_lock(file_lock)
 END_PROVIDER
 
+! These functions need to be called because internal read and write are not thread safe.
+subroutine lock_io()
+  implicit none
+  BEGIN_DOC
+! Needs to be called because before doing I/O because internal read and write
+! are not thread safe.
+  END_DOC
+  call omp_set_lock(file_lock)
+end subroutine lock_io()
 
+subroutine unlock_io()
+  implicit none
+  BEGIN_DOC
+! Needs to be called because afterdoing I/O because internal read and write
+! are not thread safe.
+  END_DOC
+  call omp_unset_lock(file_lock)
+end subroutine lock_io()

src/fci/fci.irp.f

@@ -39,12 +39,19 @@ program fci
   if (.not.is_zmq_slave) then
     PROVIDE psi_det psi_coef mo_two_e_integrals_in_map
 
+    write(json_unit,json_array_open_fmt) 'fci'
+
     if (do_pt2) then
       call run_stochastic_cipsi
     else
       call run_cipsi
     endif
 
+    write(json_unit,json_dict_uopen_fmt)
+    write(json_unit,json_dict_close_fmtx)
+    write(json_unit,json_array_close_fmtx)
+    call json_close
+
   else
     PROVIDE mo_two_e_integrals_in_map pt2_min_parallel_tasks
 

src/fci_tc_bi/NEED

@@ -1,3 +1,4 @@
+json
 tc_bi_ortho
 davidson_undressed
 cipsi_tc_bi_ortho

src/fci_tc_bi/fci_tc_bi_ortho.irp.f

@@ -62,6 +62,7 @@ subroutine run_cipsi_tc
       endif
     endif
     ! ---
+    write(json_unit,json_array_open_fmt) 'fci_tc'
 
     if (do_pt2) then
       call run_stochastic_cipsi
@@ -69,6 +70,11 @@ subroutine run_cipsi_tc
       call run_cipsi
     endif
 
+    write(json_unit,json_dict_uopen_fmt)
+    write(json_unit,json_dict_close_fmtx)
+    write(json_unit,json_array_close_fmtx)
+    call json_close
+
   else
     PROVIDE mo_bi_ortho_tc_one_e mo_bi_ortho_tc_two_e pt2_min_parallel_tasks
     if(elec_alpha_num+elec_beta_num.ge.3)then

src/fci_tc_bi/save_energy.irp.f

@@ -4,6 +4,6 @@ subroutine save_energy(E,pt2)
 ! Saves the energy in |EZFIO|.
   END_DOC
   double precision, intent(in) :: E(N_states), pt2(N_states)
-  call ezfio_set_fci_tc_energy(E(1:N_states))
+  call ezfio_set_fci_tc_bi_energy(E(1:N_states))
-  call ezfio_set_fci_tc_energy_pt2(E(1:N_states)+pt2(1:N_states))
+  call ezfio_set_fci_tc_bi_energy_pt2(E(1:N_states)+pt2(1:N_states))
 end

src/hartree_fock/NEED

@@ -1,3 +1,4 @@
 ao_one_e_ints
 ao_two_e_ints
 scf_utils
+json

src/hartree_fock/fock_matrix_hf.irp.f

@@ -15,115 +15,59 @@
  double precision, allocatable  :: ao_two_e_integral_alpha_tmp(:,:)
  double precision, allocatable  :: ao_two_e_integral_beta_tmp(:,:)
 
- ao_two_e_integral_alpha = 0.d0
+ if (do_ao_cholesky) then   ! Use Cholesky-decomposed integrals
- ao_two_e_integral_beta  = 0.d0
+   ao_two_e_integral_alpha(:,:) = ao_two_e_integral_alpha_chol(:,:)
- if (do_direct_integrals) then
+   ao_two_e_integral_beta (:,:) = ao_two_e_integral_beta_chol (:,:)
 
-   !$OMP PARALLEL DEFAULT(NONE)                                      &
+ else ! Use integrals in AO basis set
-       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,keys,values,p,q,r,s,i0,j0,k0,l0, &
-       !$OMP ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp, c0, c1, c2, &
-       !$OMP local_threshold)&
-       !$OMP SHARED(ao_num,SCF_density_matrix_ao_alpha,SCF_density_matrix_ao_beta,&
-       !$OMP ao_integrals_map,ao_integrals_threshold, ao_two_e_integral_schwartz, &
-       !$OMP ao_two_e_integral_alpha, ao_two_e_integral_beta)
 
-   allocate(keys(1), values(1))
+   ao_two_e_integral_alpha = 0.d0
-   allocate(ao_two_e_integral_alpha_tmp(ao_num,ao_num), &
+   ao_two_e_integral_beta  = 0.d0
-            ao_two_e_integral_beta_tmp(ao_num,ao_num))
+   if (do_direct_integrals) then
-   ao_two_e_integral_alpha_tmp = 0.d0
-   ao_two_e_integral_beta_tmp  = 0.d0
 
-   q = ao_num*ao_num*ao_num*ao_num
+     !$OMP PARALLEL DEFAULT(NONE)                                    &
-   !$OMP DO SCHEDULE(static,64)
+         !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,keys,values,p,q,r,s,i0,j0,k0,l0,&
-   do p=1_8,q
+         !$OMP ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp, c0, c1, c2,&
-           call two_e_integrals_index_reverse(kk,ii,ll,jj,p)
+         !$OMP local_threshold)                                      &
-           if ( (kk(1)>ao_num).or. &
+         !$OMP SHARED(ao_num,SCF_density_matrix_ao_alpha,SCF_density_matrix_ao_beta,&
-                (ii(1)>ao_num).or. &
+         !$OMP ao_integrals_map,ao_integrals_threshold, ao_two_e_integral_schwartz,&
-                (jj(1)>ao_num).or. &
+         !$OMP ao_two_e_integral_alpha, ao_two_e_integral_beta)
-                (ll(1)>ao_num) ) then
-                cycle
-           endif
-           k = kk(1)
-           i = ii(1)
-           l = ll(1)
-           j = jj(1)
 
-           logical, external :: ao_two_e_integral_zero
+     allocate(keys(1), values(1))
-           if (ao_two_e_integral_zero(i,k,j,l)) then
+     allocate(ao_two_e_integral_alpha_tmp(ao_num,ao_num),            &
-             cycle
+         ao_two_e_integral_beta_tmp(ao_num,ao_num))
-           endif
+     ao_two_e_integral_alpha_tmp = 0.d0
-           local_threshold = ao_two_e_integral_schwartz(k,l)*ao_two_e_integral_schwartz(i,j)
+     ao_two_e_integral_beta_tmp  = 0.d0
-           if (local_threshold < ao_integrals_threshold) then
-             cycle
-           endif
-           i0 = i
-           j0 = j
-           k0 = k
-           l0 = l
-           values(1) = 0.d0
-           local_threshold = ao_integrals_threshold/local_threshold
-           do k2=1,8
-             if (kk(k2)==0) then
-               cycle
-             endif
-             i = ii(k2)
-             j = jj(k2)
-             k = kk(k2)
-             l = ll(k2)
-             c0 = SCF_density_matrix_ao_alpha(k,l)+SCF_density_matrix_ao_beta(k,l)
-             c1 = SCF_density_matrix_ao_alpha(k,i)
-             c2 = SCF_density_matrix_ao_beta(k,i)
-             if ( dabs(c0)+dabs(c1)+dabs(c2) < local_threshold) then
-               cycle
-             endif
-             if (values(1) == 0.d0) then
-               values(1) = ao_two_e_integral(k0,l0,i0,j0)
-             endif
-             integral = c0 * values(1)
-             ao_two_e_integral_alpha_tmp(i,j) += integral
-             ao_two_e_integral_beta_tmp (i,j) += integral
-             integral = values(1)
-             ao_two_e_integral_alpha_tmp(l,j) -= c1 * integral
-             ao_two_e_integral_beta_tmp (l,j) -= c2 * integral
-           enddo
-   enddo
-   !$OMP END DO NOWAIT
-   !$OMP CRITICAL
-   ao_two_e_integral_alpha += ao_two_e_integral_alpha_tmp
-   ao_two_e_integral_beta  += ao_two_e_integral_beta_tmp
-   !$OMP END CRITICAL
-   deallocate(keys,values,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)
-   !$OMP END PARALLEL
- else
-   PROVIDE ao_two_e_integrals_in_map
 
-   integer(omp_lock_kind) :: lck(ao_num)
+     q = ao_num*ao_num*ao_num*ao_num
-   integer(map_size_kind)     :: i8
+     !$OMP DO SCHEDULE(static,64)
-   integer                        :: ii(8), jj(8), kk(8), ll(8), k2
+     do p=1_8,q
-   integer(cache_map_size_kind)   :: n_elements_max, n_elements
+       call two_e_integrals_index_reverse(kk,ii,ll,jj,p)
-   integer(key_kind), allocatable :: keys(:)
+       if ( (kk(1)>ao_num).or.                                       &
-   double precision, allocatable  :: values(:)
+             (ii(1)>ao_num).or.                                      &
-
+             (jj(1)>ao_num).or.                                      &
-   !$OMP PARALLEL DEFAULT(NONE)                                      &
+             (ll(1)>ao_num) ) then
-       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,n_elements_max, &
+         cycle
-       !$OMP  n_elements,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)&
+       endif
-       !$OMP SHARED(ao_num,SCF_density_matrix_ao_alpha,SCF_density_matrix_ao_beta,&
+       k = kk(1)
-       !$OMP  ao_integrals_map, ao_two_e_integral_alpha, ao_two_e_integral_beta)
+       i = ii(1)
-
+       l = ll(1)
-   call get_cache_map_n_elements_max(ao_integrals_map,n_elements_max)
+       j = jj(1)
-   allocate(keys(n_elements_max), values(n_elements_max))
-   allocate(ao_two_e_integral_alpha_tmp(ao_num,ao_num), &
-            ao_two_e_integral_beta_tmp(ao_num,ao_num))
-   ao_two_e_integral_alpha_tmp = 0.d0
-   ao_two_e_integral_beta_tmp  = 0.d0
-
-   !$OMP DO SCHEDULE(static,1)
-   do i8=0_8,ao_integrals_map%map_size
-     n_elements = n_elements_max
-     call get_cache_map(ao_integrals_map,i8,keys,values,n_elements)
-     do k1=1,n_elements
-       call two_e_integrals_index_reverse(kk,ii,ll,jj,keys(k1))
 
+       logical, external              :: ao_two_e_integral_zero
+       if (ao_two_e_integral_zero(i,k,j,l)) then
+         cycle
+       endif
+       local_threshold = ao_two_e_integral_schwartz(k,l)*ao_two_e_integral_schwartz(i,j)
+       if (local_threshold < ao_integrals_threshold) then
+         cycle
+       endif
+       i0 = i
+       j0 = j
+       k0 = k
+       l0 = l
+       values(1) = 0.d0
+       local_threshold = ao_integrals_threshold/local_threshold
        do k2=1,8
          if (kk(k2)==0) then
            cycle
@@ -132,25 +76,162 @@
          j = jj(k2)
          k = kk(k2)
          l = ll(k2)
-         integral = (SCF_density_matrix_ao_alpha(k,l)+SCF_density_matrix_ao_beta(k,l)) * values(k1)
+         c0 = SCF_density_matrix_ao_alpha(k,l)+SCF_density_matrix_ao_beta(k,l)
+         c1 = SCF_density_matrix_ao_alpha(k,i)
+         c2 = SCF_density_matrix_ao_beta(k,i)
+         if ( dabs(c0)+dabs(c1)+dabs(c2) < local_threshold) then
+           cycle
+         endif
+         if (values(1) == 0.d0) then
+           values(1) = ao_two_e_integral(k0,l0,i0,j0)
+         endif
+         integral = c0 * values(1)
          ao_two_e_integral_alpha_tmp(i,j) += integral
          ao_two_e_integral_beta_tmp (i,j) += integral
-         integral = values(k1)
+         integral = values(1)
-         ao_two_e_integral_alpha_tmp(l,j) -= SCF_density_matrix_ao_alpha(k,i) * integral
+         ao_two_e_integral_alpha_tmp(l,j) -= c1 * integral
-         ao_two_e_integral_beta_tmp (l,j) -= SCF_density_matrix_ao_beta (k,i) * integral
+         ao_two_e_integral_beta_tmp (l,j) -= c2 * integral
        enddo
      enddo
-   enddo
+     !$OMP END DO NOWAIT
-   !$OMP END DO NOWAIT
+     !$OMP CRITICAL
-   !$OMP CRITICAL
+     ao_two_e_integral_alpha += ao_two_e_integral_alpha_tmp
-   ao_two_e_integral_alpha += ao_two_e_integral_alpha_tmp
+     ao_two_e_integral_beta  += ao_two_e_integral_beta_tmp
-   ao_two_e_integral_beta  += ao_two_e_integral_beta_tmp
+     !$OMP END CRITICAL
-   !$OMP END CRITICAL
+     deallocate(keys,values,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)
-   deallocate(keys,values,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)
+     !$OMP END PARALLEL
-   !$OMP END PARALLEL
+   else
+     PROVIDE ao_two_e_integrals_in_map
 
+     integer(omp_lock_kind)         :: lck(ao_num)
+     integer(map_size_kind)         :: i8
+     integer                        :: ii(8), jj(8), kk(8), ll(8), k2
+     integer(cache_map_size_kind)   :: n_elements_max, n_elements
+     integer(key_kind), allocatable :: keys(:)
+     double precision, allocatable  :: values(:)
+
+     !$OMP PARALLEL DEFAULT(NONE)                                    &
+         !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,n_elements_max,&
+         !$OMP  n_elements,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)&
+         !$OMP SHARED(ao_num,SCF_density_matrix_ao_alpha,SCF_density_matrix_ao_beta,&
+         !$OMP  ao_integrals_map, ao_two_e_integral_alpha, ao_two_e_integral_beta)
+
+     call get_cache_map_n_elements_max(ao_integrals_map,n_elements_max)
+     allocate(keys(n_elements_max), values(n_elements_max))
+     allocate(ao_two_e_integral_alpha_tmp(ao_num,ao_num),            &
+         ao_two_e_integral_beta_tmp(ao_num,ao_num))
+     ao_two_e_integral_alpha_tmp = 0.d0
+     ao_two_e_integral_beta_tmp  = 0.d0
+
+     !$OMP DO SCHEDULE(static,1)
+     do i8=0_8,ao_integrals_map%map_size
+       n_elements = n_elements_max
+       call get_cache_map(ao_integrals_map,i8,keys,values,n_elements)
+       do k1=1,n_elements
+         call two_e_integrals_index_reverse(kk,ii,ll,jj,keys(k1))
+
+         do k2=1,8
+           if (kk(k2)==0) then
+             cycle
+           endif
+           i = ii(k2)
+           j = jj(k2)
+           k = kk(k2)
+           l = ll(k2)
+           integral = (SCF_density_matrix_ao_alpha(k,l)+SCF_density_matrix_ao_beta(k,l)) * values(k1)
+           ao_two_e_integral_alpha_tmp(i,j) += integral
+           ao_two_e_integral_beta_tmp (i,j) += integral
+           integral = values(k1)
+           ao_two_e_integral_alpha_tmp(l,j) -= SCF_density_matrix_ao_alpha(k,i) * integral
+           ao_two_e_integral_beta_tmp (l,j) -= SCF_density_matrix_ao_beta (k,i) * integral
+         enddo
+       enddo
+     enddo
+     !$OMP END DO NOWAIT
+     !$OMP CRITICAL
+     ao_two_e_integral_alpha += ao_two_e_integral_alpha_tmp
+     ao_two_e_integral_beta  += ao_two_e_integral_beta_tmp
+     !$OMP END CRITICAL
+     deallocate(keys,values,ao_two_e_integral_alpha_tmp,ao_two_e_integral_beta_tmp)
+     !$OMP END PARALLEL
+
+   endif
  endif
 
+END_PROVIDER
+
+ BEGIN_PROVIDER [ double precision, ao_two_e_integral_alpha_chol, (ao_num, ao_num) ]
+&BEGIN_PROVIDER [ double precision, ao_two_e_integral_beta_chol ,  (ao_num, ao_num) ]
+ use map_module
+ implicit none
+ BEGIN_DOC
+ ! Alpha and Beta Fock matrices in AO basis set
+ END_DOC
+
+ integer :: m,n,l,s,j
+ double precision :: integral
+ double precision, allocatable :: X(:), X2(:,:,:,:), X3(:,:,:,:)
+
+ allocate (X(cholesky_ao_num))
+
+
+ ! X(j) = \sum_{mn} SCF_density_matrix_ao(m,n) * cholesky_ao(m,n,j)
+ call dgemm('T','N',cholesky_ao_num,1,ao_num*ao_num,1.d0,            &
+     cholesky_ao, ao_num*ao_num,                                     &
+     SCF_density_matrix_ao, ao_num*ao_num,0.d0,                      &
+     X, cholesky_ao_num)
+!
+
+ ! ao_two_e_integral_alpha(m,n) = \sum_{j} cholesky_ao(m,n,j) * X(j)
+ call dgemm('N','N',ao_num*ao_num,1,cholesky_ao_num, 1.d0,           &
+     cholesky_ao, ao_num*ao_num,                                     &
+     X, cholesky_ao_num, 0.d0,                                       &
+     ao_two_e_integral_alpha_chol, ao_num*ao_num)
+
+ deallocate(X)
+
+ ao_two_e_integral_beta_chol = ao_two_e_integral_alpha_chol
+
+
+ allocate(X2(ao_num,ao_num,cholesky_ao_num,2))
+
+! ao_two_e_integral_alpha_chol (l,s) -= cholesky_ao(l,m,j) * SCF_density_matrix_ao_beta (m,n) * cholesky_ao(n,s,j)
+
+ call dgemm('N','N',ao_num,ao_num*cholesky_ao_num,ao_num, 1.d0,      &
+     SCF_density_matrix_ao_alpha, ao_num,                            &
+     cholesky_ao, ao_num, 0.d0,                                      &
+     X2(1,1,1,1), ao_num)
+
+ call dgemm('N','N',ao_num,ao_num*cholesky_ao_num,ao_num, 1.d0,      &
+     SCF_density_matrix_ao_beta, ao_num,                             &
+     cholesky_ao, ao_num, 0.d0,                                      &
+     X2(1,1,1,2), ao_num)
+
+ allocate(X3(ao_num,cholesky_ao_num,ao_num,2))
+
+ do s=1,ao_num
+  do j=1,cholesky_ao_num
+   do m=1,ao_num
+    X3(m,j,s,1) = X2(m,s,j,1)
+    X3(m,j,s,2) = X2(m,s,j,2)
+   enddo
+  enddo
+ enddo
+
+ deallocate(X2)
+
+ call dgemm('N','N',ao_num,ao_num,ao_num*cholesky_ao_num, -1.d0,     &
+     cholesky_ao, ao_num,                                            &
+     X3(1,1,1,1), ao_num*cholesky_ao_num, 1.d0,                      &
+     ao_two_e_integral_alpha_chol, ao_num)
+
+ call dgemm('N','N',ao_num,ao_num,ao_num*cholesky_ao_num, -1.d0,     &
+     cholesky_ao, ao_num,                                            &
+     X3(1,1,1,2), ao_num*cholesky_ao_num, 1.d0,                      &
+     ao_two_e_integral_beta_chol, ao_num)
+
+ deallocate(X3)
+
 END_PROVIDER
 
  BEGIN_PROVIDER [ double precision, Fock_matrix_ao_alpha, (ao_num, ao_num) ]

src/hartree_fock/scf.irp.f

@@ -80,9 +80,14 @@ subroutine run
 
   mo_label = 'Orthonormalized'
 
-  call Roothaan_Hall_SCF
+  write(json_unit,json_array_open_fmt) 'scf'
-  call ezfio_set_hartree_fock_energy(SCF_energy)
 
+  call Roothaan_Hall_SCF
+
+  write(json_unit,json_array_close_fmtx)
+  call json_close
+
+  call ezfio_set_hartree_fock_energy(SCF_energy)
 end
 
 

src/iterations/EZFIO.cfg

@@ -1,24 +0,0 @@
-[n_iter]
-interface: ezfio
-doc: Number of saved iterations
-type:integer
-default: 1
-
-[n_det_iterations]
-interface: ezfio, provider
-doc: Number of determinants at each iteration
-type: integer
-size: (100)
- 
-[energy_iterations]
-interface: ezfio, provider
-doc: The variational energy at each iteration
-type: double precision 
-size: (determinants.n_states,100)
-
-[pt2_iterations]
-interface: ezfio, provider
-doc: The |PT2| correction at each iteration
-type: double precision 
-size: (determinants.n_states,100)
-

src/iterations/io.irp.f

@@ -1,37 +0,0 @@
-BEGIN_PROVIDER [ integer, n_iter  ]
-  implicit none
-  BEGIN_DOC
-! number of iterations
-  END_DOC
-
-  logical                        :: has
-  PROVIDE ezfio_filename
-  if (mpi_master) then
-
-      double precision :: zeros(N_states,100)
-      integer :: izeros(100)
-      zeros = 0.d0
-      izeros = 0
-      call ezfio_set_iterations_n_iter(0)
-      call ezfio_set_iterations_energy_iterations(zeros)
-      call ezfio_set_iterations_pt2_iterations(zeros)
-      call ezfio_set_iterations_n_det_iterations(izeros)
-      n_iter = 1
-  endif
-  IRP_IF MPI_DEBUG
-    print *,  irp_here, mpi_rank
-    call MPI_BARRIER(MPI_COMM_WORLD, ierr)
-  IRP_ENDIF
-  IRP_IF MPI
-    include 'mpif.h'
-    integer :: ierr
-    call MPI_BCAST( n_iter, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
-    if (ierr /= MPI_SUCCESS) then
-      stop 'Unable to read n_iter with MPI'
-    endif
-  IRP_ENDIF
-
-  call write_time(6)
-
-END_PROVIDER
-

src/iterations/iterations.irp.f

@@ -1,42 +1,65 @@
-BEGIN_PROVIDER [ double precision, extrapolated_energy, (N_iter,N_states) ]
+BEGIN_PROVIDER [ integer, N_iter  ]
- implicit none
- BEGIN_DOC
- ! Extrapolated energy, using E_var = f(PT2) where PT2=0
- END_DOC
- integer :: i
- do i=1,min(N_states,N_det)
-   call extrapolate_data(N_iter,                               &
-       energy_iterations(i,1:N_iter),                          &
-          pt2_iterations(i,1:N_iter),                          &
-       extrapolated_energy(1:N_iter,i))
- enddo
-END_PROVIDER
-
-
-subroutine save_iterations(e_, pt2_,n_)
   implicit none
   BEGIN_DOC
-! Update the energy in the EZFIO file.
+! Number of CIPSI iterations
   END_DOC
-  integer, intent(in) :: n_
-  double precision, intent(in) :: e_(N_states), pt2_(N_states)
-  integer :: i
 
-  if (N_iter == 101) then
+  N_iter = 0
-    do i=2,N_iter-1
+END_PROVIDER
-      energy_iterations(1:N_states,N_iter-1) = energy_iterations(1:N_states,N_iter)
+
-      pt2_iterations(1:N_states,N_iter-1) = pt2_iterations(1:N_states,N_iter) 
+BEGIN_PROVIDER [ integer, N_iter_max ]
+ implicit none
+ BEGIN_DOC
+ ! Max number of iterations for extrapolations
+ END_DOC
+ N_iter_max = 8
+END_PROVIDER
+
+ BEGIN_PROVIDER [ double precision, energy_iterations , (n_states,N_iter_max) ]
+&BEGIN_PROVIDER [ double precision, pt2_iterations , (n_states,N_iter_max) ]
+&BEGIN_PROVIDER [ double precision, extrapolated_energy, (N_iter_max,N_states) ]
+  implicit none
+  BEGIN_DOC
+! The energy at each iteration for the extrapolations
+  END_DOC
+
+   energy_iterations = 0.d0
+   pt2_iterations = 0.d0
+   extrapolated_energy = 0.d0
+END_PROVIDER
+
+subroutine increment_n_iter(e, pt2_data)
+  use selection_types
+  implicit none
+  BEGIN_DOC
+! Does what is necessary to increment n_iter
+  END_DOC
+  double precision, intent(in) :: e(*)
+  type(pt2_type), intent(in)   :: pt2_data
+  integer :: k, i
+
+  if (N_det < N_states) return
+
+  if (N_iter < N_iter_max) then
+    N_iter += 1
+  else
+    do k=2,N_iter
+      energy_iterations(1:N_states,k-1) = energy_iterations(1:N_states,k)
+      pt2_iterations(1:N_states,k-1) = pt2_iterations(1:N_states,k)
     enddo
-    N_iter = N_iter-1
-    TOUCH N_iter
   endif
+  energy_iterations(1:N_states,N_iter) = e(1:N_states)
+  pt2_iterations(1:N_states,N_iter) = pt2_data % rpt2(1:N_states)
 
-  energy_iterations(1:N_states,N_iter) = e_(1:N_states)
+  if (N_iter < 2) then
-     pt2_iterations(1:N_states,N_iter) = pt2_(1:N_states)
+    extrapolated_energy(1,:) = energy_iterations(:,1) + pt2_iterations(:,1)
-  n_det_iterations(N_iter) = n_
+    extrapolated_energy(2,:) = energy_iterations(:,2) + pt2_iterations(:,2)
-  call ezfio_set_iterations_N_iter(N_iter)
+  else
-  call ezfio_set_iterations_energy_iterations(energy_iterations)
+    do i=1,N_states
-  call ezfio_set_iterations_pt2_iterations(pt2_iterations)
+      call extrapolate_data(N_iter,                               &
-  call ezfio_set_iterations_n_det_iterations(n_det_iterations)
+          energy_iterations(i,1:N_iter),                          &
+             pt2_iterations(i,1:N_iter),                          &
+          extrapolated_energy(1:N_iter,i))
+    enddo
+  endif
 end
-

src/iterations/print_extrapolation.irp.f

@@ -5,10 +5,14 @@ subroutine print_extrapolated_energy
   END_DOC
 
   integer :: i,k
+  integer :: N_states_p, N_iter_p
 
   if (N_iter< 2) then
     return
   endif
+  N_states_p = min(N_states,N_det)
+  N_iter_p = min(N_iter, 8)
+
   write(*,'(A)') ''
   write(*,'(A)') 'Extrapolated energies'
   write(*,'(A)') '------------------------'
@@ -20,20 +24,20 @@ subroutine print_extrapolated_energy
   write(*,*)  '=========== ', '==================='
   write(*,*)  'minimum PT2 ', 'Extrapolated energy'
   write(*,*)  '=========== ', '==================='
-  do k=2,min(N_iter,8)
+  do k=2,N_iter_p
-    write(*,'(F11.4,2X,F18.8)') pt2_iterations(1,N_iter+1-k), extrapolated_energy(k,1)
+    write(*,'(F11.4,2X,F18.8)') pt2_iterations(1,k), extrapolated_energy(k,1)
   enddo
   write(*,*)  '=========== ', '==================='
 
-  do i=2, min(N_states,N_det)
+  do i=2, N_states_p
     print *,  ''
     print *,  'State ', i
     print *,  ''
     write(*,*)  '=========== ', '=================== ', '=================== ', '==================='
     write(*,*)  'minimum PT2 ', 'Extrapolated energy ', '  Excitation (a.u)  ', '  Excitation (eV)  '
     write(*,*)  '=========== ', '=================== ', '=================== ', '==================='
-    do k=2,min(N_iter,8)
+    do k=2,N_iter_p
-      write(*,'(F11.4,X,3(X,F18.8))') pt2_iterations(i,N_iter+1-k), extrapolated_energy(k,i), &
+      write(*,'(F11.4,X,3(X,F18.8))') pt2_iterations(i,k), extrapolated_energy(k,i), &
           extrapolated_energy(k,i) - extrapolated_energy(k,1), &
           (extrapolated_energy(k,i) - extrapolated_energy(k,1) ) * 27.211396641308d0
     enddo

src/iterations_tc/EZFIO.cfg

@@ -1,24 +0,0 @@
-[n_iter]
-interface: ezfio
-doc: Number of saved iterations
-type:integer
-default: 1
-
-[n_det_iterations]
-interface: ezfio, provider
-doc: Number of determinants at each iteration
-type: integer
-size: (100)
- 
-[energy_iterations]
-interface: ezfio, provider
-doc: The variational energy at each iteration
-type: double precision 
-size: (determinants.n_states,100)
-
-[pt2_iterations]
-interface: ezfio, provider
-doc: The |PT2| correction at each iteration
-type: double precision 
-size: (determinants.n_states,100)
-

src/iterations_tc/io.irp.f

@@ -1,37 +0,0 @@
-BEGIN_PROVIDER [ integer, n_iter  ]
-  implicit none
-  BEGIN_DOC
-! number of iterations
-  END_DOC
-
-  logical                        :: has
-  PROVIDE ezfio_filename
-  if (mpi_master) then
-
-      double precision :: zeros(N_states,100)
-      integer :: izeros(100)
-      zeros = 0.d0
-      izeros = 0
-      call ezfio_set_iterations_n_iter(0)
-      call ezfio_set_iterations_energy_iterations(zeros)
-      call ezfio_set_iterations_pt2_iterations(zeros)
-      call ezfio_set_iterations_n_det_iterations(izeros)
-      n_iter = 1
-  endif
-  IRP_IF MPI_DEBUG
-    print *,  irp_here, mpi_rank
-    call MPI_BARRIER(MPI_COMM_WORLD, ierr)
-  IRP_ENDIF
-  IRP_IF MPI
-    include 'mpif.h'
-    integer :: ierr
-    call MPI_BCAST( n_iter, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
-    if (ierr /= MPI_SUCCESS) then
-      stop 'Unable to read n_iter with MPI'
-    endif
-  IRP_ENDIF
-
-  call write_time(6)
-
-END_PROVIDER
-

src/iterations_tc/iterations.irp.f

@@ -1,43 +0,0 @@
-BEGIN_PROVIDER [ double precision, extrapolated_energy, (N_iter,N_states) ]
- implicit none
- BEGIN_DOC
- ! Extrapolated energy, using E_var = f(PT2) where PT2=0
- END_DOC
-! integer :: i
- extrapolated_energy = 0.D0
-END_PROVIDER 
-
- subroutine get_extrapolated_energy(Niter,ept2,pt1,extrap_energy)
- implicit none
- integer, intent(in)  :: Niter
- double precision, intent(in) :: ept2(Niter),pt1(Niter),extrap_energy(Niter)
- call extrapolate_data(Niter,ept2,pt1,extrap_energy)
- end
-
-subroutine save_iterations(e_, pt2_,n_)
-  implicit none
-  BEGIN_DOC
-! Update the energy in the EZFIO file.
-  END_DOC
-  integer, intent(in) :: n_
-  double precision, intent(in) :: e_(N_states), pt2_(N_states)
-  integer :: i
-
-  if (N_iter == 101) then
-    do i=2,N_iter-1
-      energy_iterations(1:N_states,N_iter-1) = energy_iterations(1:N_states,N_iter)
-      pt2_iterations(1:N_states,N_iter-1) = pt2_iterations(1:N_states,N_iter) 
-    enddo
-    N_iter = N_iter-1
-    TOUCH N_iter
-  endif
-
-  energy_iterations(1:N_states,N_iter) = e_(1:N_states)
-     pt2_iterations(1:N_states,N_iter) = pt2_(1:N_states)
-  n_det_iterations(N_iter) = n_
-  call ezfio_set_iterations_N_iter(N_iter)
-  call ezfio_set_iterations_energy_iterations(energy_iterations)
-  call ezfio_set_iterations_pt2_iterations(pt2_iterations)
-  call ezfio_set_iterations_n_det_iterations(n_det_iterations)
-end
-

src/iterations_tc/print_extrapolation.irp.f

@@ -1,46 +0,0 @@
-subroutine print_extrapolated_energy
-  implicit none
-  BEGIN_DOC
-! Print the extrapolated energy in the output
-  END_DOC
-
-  integer :: i,k
-
-  if (N_iter< 2) then
-    return
-  endif
-  write(*,'(A)') ''
-  write(*,'(A)') 'Extrapolated energies'
-  write(*,'(A)') '------------------------'
-  write(*,'(A)') ''
-
-  print *,  ''
-  print *,  'State ', 1
-  print *,  ''
-  write(*,*)  '=========== ', '==================='
-  write(*,*)  'minimum PT2 ', 'Extrapolated energy'
-  write(*,*)  '=========== ', '==================='
-  do k=2,min(N_iter,8)
-    write(*,'(F11.4,2X,F18.8)') pt2_iterations(1,N_iter+1-k), extrapolated_energy(k,1)
-  enddo
-  write(*,*)  '=========== ', '==================='
-
-  do i=2, min(N_states,N_det)
-    print *,  ''
-    print *,  'State ', i
-    print *,  ''
-    write(*,*)  '=========== ', '=================== ', '=================== ', '==================='
-    write(*,*)  'minimum PT2 ', 'Extrapolated energy ', '  Excitation (a.u)  ', '  Excitation (eV)  '
-    write(*,*)  '=========== ', '=================== ', '=================== ', '==================='
-    do k=2,min(N_iter,8)
-      write(*,'(F11.4,X,3(X,F18.8))') pt2_iterations(i,N_iter+1-k), extrapolated_energy(k,i), &
-          extrapolated_energy(k,i) - extrapolated_energy(k,1), &
-          (extrapolated_energy(k,i) - extrapolated_energy(k,1) ) * 27.211396641308d0
-    enddo
-    write(*,*)  '=========== ', '=================== ', '=================== ', '==================='
-  enddo
-
-  print *,  ''
-
-end subroutine
-

src/iterations_tc/print_summary.irp.f

@@ -1,104 +0,0 @@
-subroutine print_summary(e_,pt2_data,pt2_data_err,n_det_,n_configuration_,n_st,s2_)
-  use selection_types
-  implicit none
-  BEGIN_DOC
-! Print the extrapolated energy in the output
-  END_DOC
-
-  integer, intent(in)            :: n_det_, n_configuration_, n_st
-  double precision, intent(in)   :: e_(n_st), s2_(n_st)
-  type(pt2_type)  , intent(in)   :: pt2_data, pt2_data_err
-  integer                        :: i, k
-  integer                        :: N_states_p
-  character*(9)                  :: pt2_string
-  character*(512)                :: fmt
-
-  if (do_pt2) then
-    pt2_string = '        '
-  else
-    pt2_string = '(approx)'
-  endif
-
-  N_states_p = min(N_det_,n_st)
-
-  print *, ''
-  print '(A,I12)',  'Summary at N_det = ', N_det_
-  print '(A)',      '-----------------------------------'
-  print *, ''
-
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  write(fmt,*) '(13X,', N_states_p, '(6X,A7,1X,I6,10X))'
-  write(*,fmt) ('State',k, k=1,N_states_p)
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  write(fmt,*) '(A13,', N_states_p, '(1X,F14.8,15X))'
-  write(*,fmt) '# E          ', e_(1:N_states_p)
-  if (N_states_p > 1) then
-    write(*,fmt) '# Excit. (au)', e_(1:N_states_p)-e_(1)
-    write(*,fmt) '# Excit. (eV)', (e_(1:N_states_p)-e_(1))*27.211396641308d0
-  endif
-  write(fmt,*) '(A13,', 2*N_states_p, '(1X,F14.8))'
-  write(*,fmt) '# PT2 '//pt2_string, (pt2_data % pt2(k), pt2_data_err % pt2(k), k=1,N_states_p)
-  write(*,fmt) '# rPT2'//pt2_string, (pt2_data % rpt2(k), pt2_data_err % rpt2(k), k=1,N_states_p)
-  write(*,'(A)') '#'
-  write(*,fmt) '# E+PT2      ', (e_(k)+pt2_data % pt2(k),pt2_data_err % pt2(k), k=1,N_states_p)
-  write(*,fmt) '# E+rPT2     ', (e_(k)+pt2_data % rpt2(k),pt2_data_err % rpt2(k), k=1,N_states_p)
-  if (N_states_p > 1) then
-    write(*,fmt) '# Excit. (au)', ( (e_(k)+pt2_data % pt2(k)-e_(1)-pt2_data % pt2(1)), &
-      dsqrt(pt2_data_err % pt2(k)*pt2_data_err % pt2(k)+pt2_data_err % pt2(1)*pt2_data_err % pt2(1)), k=1,N_states_p)
-    write(*,fmt) '# Excit. (eV)', ( (e_(k)+pt2_data % pt2(k)-e_(1)-pt2_data % pt2(1))*27.211396641308d0, &
-      dsqrt(pt2_data_err % pt2(k)*pt2_data_err % pt2(k)+pt2_data_err % pt2(1)*pt2_data_err % pt2(1))*27.211396641308d0, k=1,N_states_p)
-  endif
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  print *,  ''
-
-  print *,  'N_det             = ', N_det_
-  print *,  'N_states          = ', n_st
-  if (s2_eig) then
-    print *,  'N_cfg             = ', N_configuration_
-    if (only_expected_s2) then
-      print *,  'N_csf             = ', N_csf
-    endif
-  endif
-  print *,  ''
-
-  do k=1, N_states_p
-    print*,'* State ',k
-    print *,  '< S^2 >         = ', s2_(k)
-    print *,  'E               = ', e_(k)
-    print *,  'Variance        = ', pt2_data % variance(k), ' +/- ', pt2_data_err % variance(k)
-    print *,  'PT norm         = ', dsqrt(pt2_data % overlap(k,k)), ' +/- ', 0.5d0*dsqrt(pt2_data % overlap(k,k)) * pt2_data_err % overlap(k,k) / (pt2_data % overlap(k,k))
-    print *,  'PT2             = ', pt2_data % pt2(k), ' +/- ', pt2_data_err % pt2(k)
-    print *,  'rPT2            = ', pt2_data % rpt2(k), ' +/- ', pt2_data_err % rpt2(k)
-    print *,  'E+PT2 '//pt2_string//' = ', e_(k)+pt2_data % pt2(k), ' +/- ', pt2_data_err % pt2(k)
-    print *,  'E+rPT2'//pt2_string//' = ', e_(k)+pt2_data % rpt2(k), ' +/- ', pt2_data_err % rpt2(k)
-    print *,  ''
-  enddo
-
-  print *,  '-----'
-  if(n_st.gt.1)then
-    print *, 'Variational Energy difference (au | eV)'
-    do i=2, N_states_p
-      print*,'Delta E = ', (e_(i) - e_(1)), &
-        (e_(i) - e_(1)) * 27.211396641308d0
-    enddo
-    print *,  '-----'
-    print*, 'Variational + perturbative Energy difference (au | eV)'
-    do i=2, N_states_p
-      print*,'Delta E = ', (e_(i)+ pt2_data % pt2(i) - (e_(1) + pt2_data % pt2(1))), &
-        (e_(i)+ pt2_data % pt2(i) - (e_(1) + pt2_data % pt2(1))) * 27.211396641308d0
-    enddo
-    print *,  '-----'
-    print*, 'Variational + renormalized perturbative Energy difference (au | eV)'
-    do i=2, N_states_p
-      print*,'Delta E = ', (e_(i)+ pt2_data % rpt2(i) - (e_(1) + pt2_data % rpt2(1))), &
-        (e_(i)+ pt2_data % rpt2(i) - (e_(1) + pt2_data % rpt2(1))) * 27.211396641308d0
-    enddo
-  endif
-
-!  call print_energy_components()
-
-end subroutine
-

src/json/EZFIO.cfg

@@ -0,0 +1,5 @@
+[empty]
+type: logical
+doc: Needed to create the json directory
+interface: ezfio
+

src/json/NEED

@@ -0,0 +1 @@
+ezfio_files

src/json/README.rst

@@ -0,0 +1,5 @@
+====
+json
+====
+
+JSON files to simplify getting output information from QP.

src/json/json.irp.f

@@ -0,0 +1,45 @@
+BEGIN_PROVIDER [ character*(128), json_filename ]
+ implicit none
+ BEGIN_DOC
+ ! Fortran unit of the JSON file
+ END_DOC
+ integer, external            :: getUnitAndOpen
+ integer                      :: counter
+ character*(128)              :: prefix
+ logical                      :: exists
+
+ prefix = trim(ezfio_filename)//'/json/'
+
+ call lock_io
+ exists = .True.
+ counter = 0
+ do while (exists)
+   counter += 1
+   write(json_filename, '(A,I5.5,A)') trim(prefix), counter, '.json'
+   INQUIRE(FILE=trim(json_filename), EXIST=exists)
+ enddo
+ call unlock_io
+
+END_PROVIDER
+
+BEGIN_PROVIDER [ integer, json_unit]
+ implicit none
+ BEGIN_DOC
+ ! Unit file for JSON output
+ END_DOC
+ integer, external :: getUnitAndOpen
+ call ezfio_set_json_empty(.False.)
+ call lock_io
+ json_unit = getUnitAndOpen(json_filename, 'w')
+ write(json_unit, '(A)') '{'
+ call unlock_io
+END_PROVIDER
+
+subroutine json_close
+ call lock_io
+ write(json_unit, '(A)') '}'
+ close(json_unit)
+ call unlock_io
+ FREE json_unit
+end
+

src/json/json_formats.irp.f

@@ -0,0 +1,46 @@
+ BEGIN_PROVIDER [ character*(64), json_int_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_int_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_real_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_real_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_str_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_str_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_true_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_true_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_false_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_false_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_array_open_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_array_uopen_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_array_close_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_array_close_uopen_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_array_close_fmtx ]
+&BEGIN_PROVIDER [ character*(64), json_dict_open_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_dict_uopen_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_dict_close_uopen_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_dict_close_fmt ]
+&BEGIN_PROVIDER [ character*(64), json_dict_close_fmtx ]
+ implicit none
+ BEGIN_DOC
+ ! Formats for JSON output.
+ ! x: used to mark the last write (no comma)
+ END_DOC
+ json_int_fmt    = '(''   "'',A,''": '',I10,'','')'
+ json_int_fmtx   = '(''   "'',A,''": '',I10)'
+ json_real_fmt   = '(''   "'',A,''": '',E22.15,'','')'
+ json_real_fmtx  = '(''   "'',A,''": '',E22.15)'
+ json_str_fmt    = '(''   "'',A,''": "'',A,''",'')'
+ json_str_fmtx   = '(''   "'',A,''": "'',A,''"'')'
+ json_true_fmt   = '(''   "'',A,''": true,'')'
+ json_true_fmtx  = '(''   "'',A,''": true'')'
+ json_false_fmt  = '(''   "'',A,''": false,'')'
+ json_false_fmtx = '(''   "'',A,''": false'')'
+ json_array_open_fmt   = '(''   "'',A,''": ['')'
+ json_array_uopen_fmt  = '(''   ['')'
+ json_array_close_fmt  = '(''   ],'')'
+ json_array_close_uopen_fmt  = '(''   ], ['')'
+ json_array_close_fmtx = '(''   ]'')'
+ json_dict_open_fmt    = '(''   "'',A,''": {'')'
+ json_dict_uopen_fmt   = '(''   {'')'
+ json_dict_close_fmt   = '(''   },'')'
+ json_dict_close_uopen_fmt   = '(''   }, {'')'
+ json_dict_close_fmtx  = '(''   }'')'
+END_PROVIDER

src/kohn_sham/ks_scf.irp.f

@@ -90,7 +90,11 @@ subroutine run
 
 ! Choose SCF algorithm
 
+  write(json_unit,*) '"scf" : ['
   call Roothaan_Hall_SCF
+  write(json_unit,*) ']'
+
+  call json_close
 
 end
 

src/kohn_sham_rs/rs_ks_scf.irp.f

@@ -93,7 +93,10 @@ subroutine run
 
   level_shift += 1.d0
   touch level_shift
+  write(json_unit,*) '"scf" : ['
   call Roothaan_Hall_SCF
+  write(json_unit,*) ']'
+  call json_close
   call ezfio_set_kohn_sham_rs_energy(SCF_energy)
 
  write(*, '(A22,X,F16.10)') 'one_e_energy = ',one_e_energy

src/mo_two_e_ints/cholesky.irp.f

@@ -0,0 +1,16 @@
+BEGIN_PROVIDER [ double precision, cholesky_mo, (mo_num, mo_num, cholesky_ao_num) ]
+ implicit none
+ BEGIN_DOC
+ ! Cholesky vectors in MO basis
+ END_DOC
+
+ integer :: k
+
+ !$OMP PARALLEL DO PRIVATE(k)
+ do k=1,cholesky_ao_num
+  call ao_to_mo(cholesky_ao(1,1,k),ao_num,cholesky_mo(1,1,k),mo_num)
+ enddo
+ !$OMP END PARALLEL DO
+
+END_PROVIDER
+

src/mo_two_e_ints/map_integrals.irp.f

@@ -377,6 +377,7 @@ integer function load_mo_integrals(filename)
   integer*8                      :: n, j
   load_mo_integrals = 1
   open(unit=66,file=filename,FORM='unformatted',STATUS='UNKNOWN')
+  call lock_io()
   read(66,err=98,end=98) iknd, kknd
   if (iknd /= integral_kind) then
     print *,  'Wrong integrals kind in file :', iknd
@@ -399,6 +400,7 @@ integer function load_mo_integrals(filename)
     n = mo_integrals_map%map(i)%n_elements
     read(66,err=99,end=99) (key(j), j=1,n), (val(j), j=1,n)
   enddo
+  call unlock_io()
   call map_sort(mo_integrals_map)
   load_mo_integrals = 0
   return

src/mo_two_e_ints/mo_bi_integrals.irp.f

@@ -50,13 +50,16 @@ BEGIN_PROVIDER [ logical, mo_two_e_integrals_in_map ]
   call cpu_time(cpu_1)
 
   if(no_vvvv_integrals)then
-!    call four_idx_novvvv
     call four_idx_novvvv_old
   else
-    if (dble(ao_num)**4 * 32.d-9 < dble(qp_max_mem)) then
+    if (do_ao_cholesky) then
-      call four_idx_dgemm
+      call add_integrals_to_map_cholesky
     else
-      call add_integrals_to_map(full_ijkl_bitmask_4)
+      if (dble(ao_num)**4 * 32.d-9 < dble(qp_max_mem)) then
+        call four_idx_dgemm
+      else
+        call add_integrals_to_map(full_ijkl_bitmask_4)
+      endif
     endif
   endif
 
@@ -175,7 +178,7 @@ subroutine add_integrals_to_map(mask_ijkl)
   implicit none
 
   BEGIN_DOC
-  ! Adds integrals to tha MO map according to some bitmask
+  ! Adds integrals to the MO map according to some bitmask
   END_DOC
 
   integer(bit_kind), intent(in)  :: mask_ijkl(N_int,4)
@@ -450,13 +453,72 @@ subroutine add_integrals_to_map(mask_ijkl)
 
 end
 
+subroutine add_integrals_to_map_cholesky
+  use bitmasks
+  implicit none
+
+  BEGIN_DOC
+  ! Adds integrals to the MO map using Cholesky vectors
+  END_DOC
+
+  integer :: i,j,k,l,m
+  integer :: size_buffer, n_integrals
+  size_buffer = min(mo_num*mo_num*mo_num,16000000)
+
+  double precision, allocatable :: Vtmp(:,:,:,:)
+  integer(key_kind)  , allocatable :: buffer_i(:)
+  real(integral_kind), allocatable :: buffer_value(:)
+
+  if (.True.) then
+    ! In-memory transformation
+
+    allocate (Vtmp(mo_num,mo_num,mo_num,mo_num))
+
+    call dgemm('N','T',mo_num*mo_num,mo_num*mo_num,cholesky_ao_num,1.d0, &
+       cholesky_mo, mo_num*mo_num, &
+       cholesky_mo, mo_num*mo_num, 0.d0, &
+       Vtmp, mo_num*mo_num)
+
+    !$OMP PARALLEL PRIVATE(i,j,k,l,n_integrals,buffer_value, buffer_i)
+    allocate (buffer_i(size_buffer), buffer_value(size_buffer))
+    n_integrals = 0
+    !$OMP DO
+    do l=1,mo_num
+      do k=1,l
+        do j=1,mo_num
+          do i=1,j
+            if (abs(Vtmp(i,j,k,l)) > mo_integrals_threshold) then
+              n_integrals += 1
+              buffer_value(n_integrals) = Vtmp(i,j,k,l)
+              !DIR$ FORCEINLINE
+              call mo_two_e_integrals_index(i,k,j,l,buffer_i(n_integrals))
+              if (n_integrals == size_buffer) then
+                call map_append(mo_integrals_map, buffer_i, buffer_value, n_integrals)
+                n_integrals = 0
+              endif
+            endif
+          enddo
+        enddo
+      enddo
+    enddo
+    !$OMP END DO
+    call map_append(mo_integrals_map, buffer_i, buffer_value, n_integrals)
+    deallocate(buffer_i, buffer_value)
+    !$OMP END PARALLEL
+
+    deallocate(Vtmp)
+    call map_unique(mo_integrals_map)
+
+  endif
+
+end
 
 subroutine add_integrals_to_map_three_indices(mask_ijk)
   use bitmasks
   implicit none
 
   BEGIN_DOC
-  ! Adds integrals to tha MO map according to some bitmask
+  ! Adds integrals to the MO map according to some bitmask
   END_DOC
 
   integer(bit_kind), intent(in)  :: mask_ijk(N_int,3)

src/nuclei/nuclei.irp.f

@@ -241,13 +241,13 @@ END_PROVIDER
      enddo
      character*(80)                 :: buffer, dummy
      do
-     read(iunit,'(A80)',end=10) buffer
+       read(iunit,'(A80)',end=10) buffer
-     read(buffer,*) i ! First read i
+       read(buffer,*) i ! First read i
-     read(buffer,*) i, element_name(i), dummy, element_mass(i)
+       read(buffer,*) i, element_name(i), dummy, element_mass(i)
-   enddo
+     enddo
-   10 continue
+     10 continue
-   close(10)
+     close(10)
- endif
+   endif
 
  IRP_IF MPI_DEBUG
    print *,  irp_here, mpi_rank

src/scf_utils/NEED

@@ -1,2 +1,3 @@
 mo_guess 
 bitmask 
+json

src/scf_utils/roothaan_hall_scf.irp.f

@@ -12,6 +12,7 @@ END_DOC
 
   integer                        :: iteration_SCF,dim_DIIS,index_dim_DIIS
 
+  logical                        :: converged
   integer                        :: i,j
   logical, external              :: qp_stop
   double precision, allocatable :: mo_coef_save(:,:)
@@ -50,10 +51,8 @@ END_DOC
 !
   PROVIDE FPS_SPF_matrix_AO Fock_matrix_AO 
 
-  do while ( &
+  converged = .False.
-    ( (max_error_DIIS > threshold_DIIS_nonzero) .or. &
+  do while ( .not.converged .and. (iteration_SCF < n_it_SCF_max) )
-      (dabs(Delta_energy_SCF) > thresh_SCF) &
-    ) .and. (iteration_SCF < n_it_SCF_max) )
 
 ! Increment cycle number
 
@@ -144,17 +143,49 @@ END_DOC
     SOFT_TOUCH level_shift
     energy_SCF_previous = energy_SCF
 
+    converged = ( (max_error_DIIS <= threshold_DIIS_nonzero) .and. &
+                  (dabs(Delta_energy_SCF) <= thresh_SCF) )
+
 !   Print results at the end of each iteration
 
     write(6,'(I4, 1X, F16.10, 1X, F16.10, 1X, F16.10, 1X, F16.10, 1X, I3)')  &
       iteration_SCF, energy_SCF, Delta_energy_SCF, max_error_DIIS, level_shift, dim_DIIS
 
+!   Write data in JSON file
+
+    call lock_io
+    if (iteration_SCF == 1) then
+      write(json_unit, json_dict_uopen_fmt)
+    else
+      write(json_unit, json_dict_close_uopen_fmt)
+    endif
+    write(json_unit, json_int_fmt) 'iteration', iteration_SCF
+    write(json_unit, json_real_fmt) 'energy', energy_SCF
+    write(json_unit, json_real_fmt) 'delta_energy_SCF', Delta_energy_SCF
+    write(json_unit, json_real_fmt) 'max_error_DIIS', max_error_DIIS
+    write(json_unit, json_real_fmt) 'level_shift', level_shift
+    write(json_unit, json_int_fmt) 'dim_DIIS', dim_DIIS
+    call unlock_io
+
     if (Delta_energy_SCF < 0.d0) then
       call save_mos
+      write(json_unit, json_true_fmt) 'saved'
+    else
+      write(json_unit, json_false_fmt) 'saved'
     endif
+
+    call lock_io
+    if (converged) then
+      write(json_unit, json_true_fmtx) 'converged'
+    else
+      write(json_unit, json_false_fmtx) 'converged'
+    endif
+    call unlock_io
+
     if (qp_stop()) exit
 
   enddo
+  write(json_unit, json_dict_close_fmtx)
 
  if (iteration_SCF < n_it_SCF_max) then
    mo_label = 'Canonical'
@@ -166,6 +197,10 @@ END_DOC
   write(6,'(A4, 1X, A16, 1X, A16, 1X, A16, 1X, A16)')  &
     '====','================','================','================','================'
   write(6,*)
+  if (converged) then
+    write(6,*) 'SCF converged'
+  endif
+
 
   if(.not.frozen_orb_scf)then
    call mo_as_eigvectors_of_mo_matrix(Fock_matrix_mo,size(Fock_matrix_mo,1), &

src/tc_bi_ortho/h_tc_s2_u0.irp.f

@@ -152,7 +152,7 @@ subroutine H_tc_s2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishi
   use bitmasks
   implicit none
   BEGIN_DOC
-  ! Computes $v_t = H | u_t\rangle$ 
+  ! Computes $v_t = H | u_t\rangle$
   !
   ! Default should be 1,N_det,0,1
   !
@@ -160,7 +160,7 @@ subroutine H_tc_s2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishi
   END_DOC
   integer, intent(in)            :: N_st,sze,istart,iend,ishift,istep
   double precision, intent(in)   :: u_t(N_st,N_det)
-  logical, intent(in)             :: do_right 
+  logical, intent(in)             :: do_right
   double precision, intent(out)  :: v_t(N_st,sze), s_t(N_st,sze)
 
 
@@ -193,7 +193,7 @@ subroutine H_tc_s2_u_0_nstates_openmp_work_$N_int(v_t,s_t,u_t,N_st,sze,istart,ie
   END_DOC
   integer, intent(in)            :: N_st,sze,istart,iend,ishift,istep
   double precision, intent(in)   :: u_t(N_st,N_det)
-  logical, intent(in)            :: do_right 
+  logical, intent(in)            :: do_right
   double precision, intent(out)  :: v_t(N_st,sze), s_t(N_st,sze)
 
   double precision               :: hij, sij
@@ -570,7 +570,7 @@ compute_singles=.True.
         lrow = psi_bilinear_matrix_rows(l_a)
         ASSERT (lrow <= N_det_alpha_unique)
 
-        tmp_det2(1:N_int,1) = psi_det_alpha_unique(1:N_int, lrow) 
+        tmp_det2(1:N_int,1) = psi_det_alpha_unique(1:N_int, lrow)
 !        call i_H_j( tmp_det, tmp_det2, $N_int, hij)
 !        call i_H_j_double_spin( tmp_det(1,1), psi_det_alpha_unique(1, lrow), $N_int, hij)
         if(do_right)then
@@ -721,7 +721,7 @@ compute_singles=.True.
         lcol = psi_bilinear_matrix_transp_columns(l_b)
         ASSERT (lcol <= N_det_beta_unique)
 
-        tmp_det2(1:N_int,2) = psi_det_beta_unique(1:N_int, lcol) 
+        tmp_det2(1:N_int,2) = psi_det_beta_unique(1:N_int, lcol)
 !        call i_H_j( tmp_det, tmp_det2, $N_int, hij)
 !        call i_H_j_double_spin( tmp_det(1,2), psi_det_beta_unique(1, lcol), $N_int, hij)
         if(do_right)then

src/tools/print_e_conv.irp.f

@@ -1,80 +0,0 @@
-program print_e_conv
- implicit none
- BEGIN_DOC
-! program that prints in a human readable format the convergence of the CIPSI algorithm.
-!
-! for all istate, this program produces
-!
-! * a file "EZFIO.istate.conv" containing the variational and var+PT2 energies as a function of N_det
-!
-! * for istate > 1, a file EZFIO.istate.delta_e.conv containing the energy difference (both var and var+PT2) with the ground state as a function of N_det
- END_DOC
-
-  provide ezfio_filename
-  call routine_e_conv
- end
-
-subroutine routine_e_conv
- implicit none
- BEGIN_DOC
-! routine called by :c:func:`print_e_conv`
- END_DOC
- integer :: N_iter_tmp
- integer :: i,istate
- character*(128) :: output
- integer :: i_unit_output,getUnitAndOpen
- character*(128) :: filename
-
- integer, allocatable :: n_det_tmp(:)
- call ezfio_get_iterations_N_iter(N_iter_tmp)
- print*,'N_iter_tmp = ',N_iter_tmp
- double precision, allocatable :: e(:,:),pt2(:,:)
- allocate(e(N_states, 100),pt2(N_states, 100),n_det_tmp(100))
- call ezfio_get_iterations_energy_iterations(e)
- call ezfio_get_iterations_pt2_iterations(pt2)
- call ezfio_get_iterations_n_det_iterations(n_det_tmp)
-
-
-  do istate = 1, N_states
-   if (istate.lt.10)then
-    write (filename, "(I1)")istate
-   else
-    write (filename, "(I2)")istate
-   endif
-   print*,filename
-   output=trim(ezfio_filename)//'.'//trim(filename)//'.conv'
-   output=trim(output)
-   print*,'output = ',trim(output)
-   i_unit_output = getUnitAndOpen(output,'w')
-   write(i_unit_output,*)'# N_det    E_var        E_var + PT2'
-   do i = 1, N_iter_tmp
-    write(i_unit_output,'(I9,X,3(F16.10,X))')n_det_tmp(i),e(istate,i),e(istate,i) + pt2(istate,i)
-   enddo
-  enddo
-
-  if(N_states.gt.1)then
-   double precision, allocatable :: deltae(:,:),deltae_pt2(:,:)
-   allocate(deltae(N_states,100),deltae_pt2(N_states,100))
-   do i = 1, N_iter_tmp
-    do istate = 1, N_states
-     deltae(istate,i) = e(istate,i) - e(1,i)
-     deltae_pt2(istate,i) = e(istate,i) + pt2(istate,i) - (e(1,i) + pt2(1,i))
-    enddo
-   enddo
-   do istate = 2, N_states
-     if (istate.lt.10)then
-      write (filename, "(I1)")istate
-     else
-      write (filename, "(I2)")istate
-     endif
-     output=trim(ezfio_filename)//'.'//trim(filename)//'.delta_e.conv'
-     print*,'output = ',trim(output)
-     i_unit_output = getUnitAndOpen(output,'w')
-     write(i_unit_output,*)'# N_det    Delta E_var   Delta (E_var + PT2)'
-     do i = 1, N_iter_tmp
-      write(i_unit_output,'(I9,X,100(F16.10,X))')n_det_tmp(i),deltae(istate,i),deltae_pt2(istate,i)
-     enddo
-   enddo
-  endif
-
-end

src/two_body_rdm/io_two_rdm.irp.f

@@ -1,15 +1,17 @@
 subroutine write_array_two_rdm(n_orb,nstates,array_tmp,name_file)
  implicit none
  integer, intent(in) :: n_orb,nstates
- character*(128),  intent(in) :: name_file 
+ character*(128),  intent(in) :: name_file
  double precision, intent(in) :: array_tmp(n_orb,n_orb,n_orb,n_orb,nstates)
 
  character*(128)                :: output
  integer                        :: i_unit_output,getUnitAndOpen
- PROVIDE ezfio_filename                                                                                                  
+ PROVIDE ezfio_filename
  output=trim(ezfio_filename)//'/work/'//trim(name_file)
  i_unit_output = getUnitAndOpen(output,'W')
+ call lock_io()
  write(i_unit_output)array_tmp
+ call unlock_io()
  close(unit=i_unit_output)
 end
 
@@ -18,12 +20,14 @@ subroutine read_array_two_rdm(n_orb,nstates,array_tmp,name_file)
  character*(128)                :: output
  integer                        :: i_unit_output,getUnitAndOpen
  integer, intent(in) :: n_orb,nstates
- character*(128),  intent(in)  :: name_file 
+ character*(128),  intent(in)  :: name_file
  double precision, intent(out) :: array_tmp(n_orb,n_orb,n_orb,n_orb,N_states)
- PROVIDE ezfio_filename                                                                                                  
+ PROVIDE ezfio_filename
  output=trim(ezfio_filename)//'/work/'//trim(name_file)
  i_unit_output = getUnitAndOpen(output,'R')
+ call lock_io()
  read(i_unit_output)array_tmp
+ call unlock_io()
  close(unit=i_unit_output)
 end
 

src/utils/format_w_error.irp.f

@@ -1,7 +1,7 @@
 subroutine format_w_error(value,error,size_nb,max_nb_digits,format_value,str_error)
 
   implicit none
- 
+
   BEGIN_DOC
   ! Format for double precision, value(error)
   END_DOC
@@ -14,7 +14,7 @@ subroutine format_w_error(value,error,size_nb,max_nb_digits,format_value,str_err
 
   ! out
   ! | format_value  | character | string FX.Y for the format |
-  ! | str_error     | character | string of the error |
+  ! | str_error     | character | string of the error        |
 
   ! internal
   ! | str_size      | character | size in string format                             |
@@ -33,6 +33,7 @@ subroutine format_w_error(value,error,size_nb,max_nb_digits,format_value,str_err
   character(len=20)              :: str_size, str_nb_digits, str_exp
   integer                        :: nb_digits
 
+  call lock_io()
   ! max_nb_digit: Y max
   ! size_nb = Size of the double: X (FX.Y)
   write(str_size,'(I3)') size_nb
@@ -40,17 +41,17 @@ subroutine format_w_error(value,error,size_nb,max_nb_digits,format_value,str_err
   ! Error
   write(str_exp,'(1pE20.0)') error
   str_error = trim(adjustl(str_exp))
-  
+
   ! Number of digit: Y (FX.Y) from the exponent
   str_nb_digits = str_exp(19:20)
   read(str_nb_digits,*) nb_digits
- 
+
   ! If the error is 0d0
-  if (error <= 1d-16) then 
+  if (error <= 1d-16) then
     write(str_nb_digits,*) max_nb_digits
   endif
 
-  ! If the error is too small 
+  ! If the error is too small
   if (nb_digits > max_nb_digits) then
       write(str_nb_digits,*) max_nb_digits
       str_error(1:1) = '0'
@@ -65,7 +66,8 @@ subroutine format_w_error(value,error,size_nb,max_nb_digits,format_value,str_err
   ! FX.Y,A1,A1,A1 for value(str_error)
   !string = 'F'//trim(adjustl(str_size))//'.'//trim(adjustl(str_nb_digits))//',A1,A1,A1'
 
-  ! FX.Y just for the value 
+  ! FX.Y just for the value
   format_value = 'F'//trim(adjustl(str_size))//'.'//trim(adjustl(str_nb_digits))
+  call unlock_io()
 
 end

src/utils/linear_algebra.irp.f

@@ -1854,7 +1854,7 @@ do k = 1, N
 end do
 ! TODO: It should be possible to use only one vector of size (1:rank) as a buffer
 ! to do the swapping in-place
-U = 0.00D+0
+U(:,:) = 0.00D+0
 do k = 1, N
   l = piv(k)
   U(l, :) = A(1:rank, k)

src/utils/memory.irp.f

@@ -8,7 +8,9 @@ BEGIN_PROVIDER [ integer, qp_max_mem ]
  qp_max_mem = 2000
  call getenv('QP_MAXMEM',env)
  if (trim(env) /= '') then
+    call lock_io()
     read(env,*) qp_max_mem
+    call unlock_io()
  endif
  call write_int(6,qp_max_mem,'Target maximum memory (GB)')
 
@@ -25,7 +27,7 @@ subroutine resident_memory(value)
   character*(32) :: key
   double precision, intent(out) :: value
 
-  call omp_set_lock(file_lock)
+  call lock_io()
   call usleep(10)
 
   value = 0.d0
@@ -40,7 +42,7 @@ subroutine resident_memory(value)
   20 continue
   close(iunit)
   value = value / (1024.d0*1024.d0)
-  call omp_unset_lock(file_lock)
+  call unlock_io()
 end function
 
 subroutine total_memory(value)
@@ -53,6 +55,7 @@ subroutine total_memory(value)
   character*(32) :: key
   double precision, intent(out) :: value
 
+  call lock_io()
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
     read(iunit,*,err=10,end=20) key, value
@@ -64,6 +67,7 @@ subroutine total_memory(value)
   20 continue
   close(iunit)
   value = value / (1024.d0*1024.d0)
+  call unlock_io()
 end function
 
 double precision function memory_of_double(n)