documentation batch 3 (#298)

filippi-claudia · Oct 2, 2024 · e575acc · e575acc
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diff --git a/src/vmc/CMakeLists.txt b/src/vmc/CMakeLists.txt
@@ -116,8 +116,8 @@ if (MPI_Fortran_FOUND)
     lapack_wrapper.f90
     main.f90
     matinv.f90
-    new_parser_read_data.f90
-    read_trexio_data.f90
+    read_data_parser.f90
+    read_data_trexio.f90
     fitting.f90
     olbfgs.f90
     optgeo_convcartzmat.f90
@@ -140,7 +140,7 @@ if (MPI_Fortran_FOUND)
     )
 
   set_property(
-  SOURCE new_parser_read_data.f90
+  SOURCE read_data_parser.f90
   APPEND
   PROPERTY COMPILE_DEFINITIONS
   CMAKE_Fortran_COMPILER=\"${CMAKE_Fortran_COMPILER}\"
@@ -153,7 +153,7 @@ if (MPI_Fortran_FOUND)
 
   set(ENABLE_GPU ${ENABLE_GPU} PARENT_SCOPE)
   message (STATUS "GPU IS ENABLED")
-  
+
   set(ENABLE_TREXIO ${ENABLE_TREXIO} PARENT_SCOPE)
   set(ENABLE_QMCKL  ${ENABLE_QMCKL} PARENT_SCOPE)
 
@@ -194,8 +194,8 @@ if (MPI_Fortran_FOUND)
     ${CMAKE_CURRENT_SOURCE_DIR}/optgeo_convcartzmat.f90
     ${CMAKE_CURRENT_SOURCE_DIR}/optgeo_coords_int.f90
     ${CMAKE_CURRENT_SOURCE_DIR}/optgeo_hessian.f90
-    ${CMAKE_CURRENT_SOURCE_DIR}/new_parser_read_data.f90
-    ${CMAKE_CURRENT_SOURCE_DIR}/read_trexio_data.f90
+    ${CMAKE_CURRENT_SOURCE_DIR}/read_data_parser.f90
+    ${CMAKE_CURRENT_SOURCE_DIR}/read_data_trexio.f90
     ${CMAKE_CURRENT_SOURCE_DIR}/set_input_data.f90
     ${CMAKE_CURRENT_SOURCE_DIR}/pot_local.f90
     ${CMAKE_CURRENT_SOURCE_DIR}/pcm_3dgrid.f90

diff --git a/src/vmc/basis_fns.f90 b/src/vmc/basis_fns.f90
@@ -1,11 +1,11 @@
+!> calculate the values of the basis functions and their derivatives
+!> ider = 0 -> value
+!> ider = 1 -> value, gradient
+!> ider = 2 -> value, gradient, laplacian
+!> ider = 3 -> value, gradient, laplacian, forces
 module basis_fns_mod
 contains
       subroutine basis_fns(ie1,ie2,ncoord,rvec_en,r_en,ider)
-! calculate the values of the basis functions and their derivatives
-! ider = 0 -> value
-! ider = 1 -> value, gradient
-! ider = 2 -> value, gradient, laplacian
-! ider = 3 -> value, gradient, laplacian, forces
 
       use m_force_analytic, only: iforce_analy
       use multiple_geo, only: iwf
@@ -229,6 +229,7 @@ subroutine basis_fns(ie1,ie2,ncoord,rvec_en,r_en,ider)
       return
       end
 !-------------------------------------------------------------------
+      !> Calculates the wavefunction and its derivatives and laplacian
       subroutine phi_combine(l,xc,ri,ri2,wfv,y,dy,ddy,ddy_lap,dlapy,phi,dphi,d2phi,d2phi_all,d3phi,ider)
       use precision_kinds, only: dp
       implicit none
@@ -310,6 +311,7 @@ subroutine phi_combine(l,xc,ri,ri2,wfv,y,dy,ddy,ddy_lap,dlapy,phi,dphi,d2phi,d2p
       return
       end
 !-------------------------------------------------------------------
+      !> n0_inc subroutine
       subroutine n0_inc(l,k,ic)
 
       use phifun,  only: dphin,n0_ibasis,n0_ic,n0_nbasis,phin

diff --git a/src/vmc/commands.p2 b/src/vmc/commands.p2
diff --git a/src/vmc/cuspexact4.f90 b/src/vmc/cuspexact4.f90
@@ -1,7 +1,37 @@
+!> The last 2 columns are what we care about in the foll. table
+!>------------------------------------------------------------------------------
+!> ord  # of   cumul.    # terms  # terms   # 3-body  Cumul. #      Cumul # indep
+!>      terms  # terms   even t   odd t      terms    3-body terms  3-body terms
+!>  n  (n+1)* (n^3+5n)/6         int((n+1)/2            nterms
+!>    (n+2)/2  +n^2+n           *int((n+2)/2
+!>------------------------------------------------------------------------------
+!>  1     3       3        2         1          0         0              0
+!>  2     6       9        4         2          2         2              0
+!>  3    10      19        6         4          4         6              2
+!>  4    15      34        9         6          7        13              7
+!>  5    21      55       12         9         10        23             15
+!>  6    28      83       16        12         14        37             27
+!>  7    36     119       20        16         18        55             43
+!>------------------------------------------------------------------------------
+!>
+!> Dependent coefs. fixed by e-e and e-n cusp conditions resp. are;
+!> order:   2  3  4  5  6  7  2  3  4  5  6  7
+!> coefs:   1  4 10 19 32 49  2  6 12 22 35 53
+!>
+!> So the terms varied for a 5th, 6th order polynomial are:
+!>    3   5   7 8 9    11    13 14 15 16 17 18    20 21    23 (iwjasc(iparm),iparm=1,nparmc)
+!>    3   5   7 8 9    11    13 14 15 16 17 18    20 21    23 24 25 26 27 28 29 30 31    33 34    36 37
+!>                                                                 (iwjasc(iparm),iparm=1,nparmc)
+!>
+!>
+!> All the dependent variables, except one (the one from the 2nd order
+!> e-n cusp) depend only on independent variables.  On the other hand
+!> the one from the 2nd order e-n cusp depends only on other dependent
+!> variables.
+!>@author Cyrus Umrigar
 module cuspexact4_mod
 contains
       subroutine cuspexact4(iprin,iadiag)
-! Written by Cyrus Umrigar
       use cuspmat4, only: d,iwc4,nterms
       use jastrow, only: c,nordc
       use precision_kinds, only: dp
@@ -11,39 +41,6 @@ subroutine cuspexact4(iprin,iadiag)
       integer :: i, iadiag, iprin, it, j
       real(dp) :: sum
 
-
-
-! The last 2 columns are what we care about in the foll. table
-!------------------------------------------------------------------------------
-! ord  # of   cumul.    # terms  # terms   # 3-body  Cumul. #      Cumul # indep
-!      terms  # terms   even t   odd t      terms    3-body terms  3-body terms
-!  n  (n+1)* (n^3+5n)/6         int((n+1)/2            nterms
-!    (n+2)/2  +n^2+n           *int((n+2)/2
-!------------------------------------------------------------------------------
-!  1     3       3        2         1          0         0              0
-!  2     6       9        4         2          2         2              0
-!  3    10      19        6         4          4         6              2
-!  4    15      34        9         6          7        13              7
-!  5    21      55       12         9         10        23             15
-!  6    28      83       16        12         14        37             27
-!  7    36     119       20        16         18        55             43
-!------------------------------------------------------------------------------
-
-! Dependent coefs. fixed by e-e and e-n cusp conditions resp. are;
-! order:   2  3  4  5  6  7  2  3  4  5  6  7
-! coefs:   1  4 10 19 32 49  2  6 12 22 35 53
-
-! So the terms varied for a 5th, 6th order polynomial are:
-!    3   5   7 8 9    11    13 14 15 16 17 18    20 21    23 (iwjasc(iparm),iparm=1,nparmc)
-!    3   5   7 8 9    11    13 14 15 16 17 18    20 21    23 24 25 26 27 28 29 30 31    33 34    36 37
-!                                                                 (iwjasc(iparm),iparm=1,nparmc)
-
-
-! All the dependent variables, except one (the one from the 2nd order
-! e-n cusp) depend only on independent variables.  On the other hand
-! the one from the 2nd order e-n cusp depends only on other dependent
-! variables.
-
       do it=1,nctype
 
 ! Set dep. variables from e-e cusp

diff --git a/src/vmc/davidson_wrap.f90 b/src/vmc/davidson_wrap.f90
@@ -1,17 +1,18 @@
+!>----------------------------------------------------------------------------
+!>
+!> ... iterative solution of the eigenvalue problem:
+!>
+!> ... ( H - e S ) * v = 0
+!>
+!> ... where H is an hermitean operator, e is a real scalar,
+!> ... S is an symmetric matrix, v is a real vector
+!> ... (real wavefunctions with only half plane waves stored)
+!>
 module davidson_wrap_mod
 contains
 SUBROUTINE davidson_wrap(nparm, nparmx, nvec, nvecx, mvec, eigenvectors, ethr, &
                          eigenvalues, btype, notcnv, dav_iter, ipr, method)
-    !----------------------------------------------------------------------------
-    !
-    ! ... iterative solution of the eigenvalue problem:
-    !
-    ! ... ( H - e S ) * v = 0
-    !
-    ! ... where H is an hermitean operator, e is a real scalar,
-    ! ... S is an symmetric matrix, v is a real vector
-    ! ... (real wavefunctions with only half plane waves stored)
-    !
+
       use array_utils, only: eye,write_matrix,write_vector
       use contrl_file, only: errunit,ounit
       use davidson, only: davidson_parameters,fun_mtx_gemv,fun_stx_gemv
@@ -23,7 +24,6 @@ SUBROUTINE davidson_wrap(nparm, nparmx, nvec, nvecx, mvec, eigenvectors, ethr, &
 
     IMPLICIT NONE
 
-
     !> \param npram dimension of the matrix to be diagonalized
     !> \param nparmx leading dimension of matrix eigenvectors
     !> \param nvec integer number of searched low-lying roots

diff --git a/src/vmc/dumper.f90 b/src/vmc/dumper.f90
@@ -1,8 +1,8 @@
+!> MPI version created by Claudia Filippi starting from serial version
+!> routine to pick up and dump everything needed to restart
+!> job where it left off
+!> @author Claudia Filippi
 module dumper_mod
-! MPI version created by Claudia Filippi starting from serial version
-! routine to pick up and dump everything needed to restart
-! job where it left off
-
       use config, only: xold
       use contrl_file,    only: ounit
       use csfs, only: nstates
@@ -47,6 +47,7 @@ module dumper_mod
       implicit none
 
 contains
+      !> routine to dump everything needed to restart
       subroutine dumper
       implicit none
       integer :: i, id, idfrom, idget, ierr
@@ -102,6 +103,7 @@ subroutine dumper
       end subroutine
 
 !-----------------------------------------------------------------------
+      !> routine to pick up everything needed to restart
       subroutine startr
       implicit none
       integer :: i, id, idfrom, idget, ierr

diff --git a/src/vmc/dumper_more.f90 b/src/vmc/dumper_more.f90
@@ -1,4 +1,5 @@
-      module dumper_more_mod
+    !> Module to dump and restart data for a calculation
+    module dumper_more_mod
 
       use basis,   only: zex
       use constants, only: hb
@@ -54,6 +55,7 @@ module dumper_more_mod
       implicit none
 
 contains
+      !> \brief Dumps the data to a file
       subroutine dumper_more
       implicit none
       integer :: i, ib, ic, ifr, istate
@@ -118,6 +120,7 @@ subroutine dumper_more
       end subroutine
 
 !-----------------------------------------------------------------------
+      !> \brief Restarts the data from a file
       subroutine startr_more
       implicit none
       integer :: i, ib, ic, ifr, istate

diff --git a/src/vmc/ewald.f90 b/src/vmc/ewald.f90
@@ -345,14 +345,15 @@ subroutine set_ewald
       end
 !-----------------------------------------------------------------------
 
+!> Written by Cyrus Umrigar
+!> distcell(i) is the perpendicular distance between cell faces parallel
+!> to the other 2 directions from i.
+!> dist_min is the shortest of these three.
+!> By choosing the range of the short-range part of the Ewald sums to be
+!> <= half the shortest perpendicular distance we ensure that the short-range
+!> part has zero or one terms.
       subroutine short_distance(vector,volume,dist_min,distcell)
-! Written by Cyrus Umrigar
-! distcell(i) is the perpendicular distance between cell faces parallel
-! to the other 2 directions from i.
-! dist_min is the shortest of these three.
-! By choosing the range of the short-range part of the Ewald sums to be
-! <= half the shortest perpendicular distance we ensure that the short-range
-! part has zero or one terms.
+
       use contrl_file,    only: ounit
       use precision_kinds, only: dp
       implicit none
@@ -407,8 +408,9 @@ subroutine short_distance(vector,volume,dist_min,distcell)
       end
 !-----------------------------------------------------------------------
 
+!> evaluates the cross-product of v1 and v2 and puts it in v3
+!> @author Edgar Josue Landinez Borda
       subroutine cross(v1,v2,v3)
-! evaluates the cross-product of v1 and v2 and puts it in v3
 
       use precision_kinds, only: dp
       implicit none
@@ -1510,7 +1512,7 @@ subroutine dvlrange_ee(ngnorm,gnorm,igmult,cos_sum,sin_sum,dcos_g,dsin_g,ddcos_g
        enddo
        ddvl=ddvl+2*y(1)*(ddcos_g(ir,ivec)*cos_sum(1)+ddsin_g(ir,ivec)*sin_sum(1)+gnorm(1)*gnorm(1))
       enddo
-      
+
       do k=2,ngnorm
         do im=1,igmult(k)
           ivec=ivec+1

diff --git a/src/vmc/fitting.f90 b/src/vmc/fitting.f90
@@ -1,3 +1,4 @@
+    !> Module for fitting methods.
     module fitting_methods
 
         implicit none
@@ -8,10 +9,10 @@ module fitting_methods
         contains
 
         subroutine exp_fit(x, y, n, a, b)
-!! This subroutine takes an array of floating point numbers and fits them to
-!! an exponential function in the form of y = a*exp(-b*x).
-!! @Author: Ravindra Shinde
-!! @Date:   Tue May 18 13:54:00 EDT 2022
+!> This subroutine takes an array of floating point numbers and fits them to
+!> an exponential function in the form of y = a*exp(-b*x).
+!> @author: Ravindra Shinde
+!> @date:   Tue May 18 13:54:00 EDT 2022
 !> \param[in] x: Array of floating point numbers.
 !> \param[in] y: Array of floating point numbers.
 !> \param[in] n: Number of elements in x or y.
@@ -43,7 +44,7 @@ subroutine exp_fit(x, y, n, a, b)
         xx_sum = 0.0
 
         do i = 1, n
-            
+
             w(i) = log(dabs(y(i)))
             x_sum = x_sum + x(i)
             y_sum = y_sum + y(i)

diff --git a/src/vmc/gauss.f90 b/src/vmc/gauss.f90
@@ -1,14 +1,13 @@
 module gauss_mod
 contains
       function gauss()
-! Written by Cyrus Umrigar
-!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-! Generate a gaussian random number using Box-Mueller method.
-! Rewrote inline function as a function so that there would be no ambiquity as to
-! the order in which the 2 rannyu's are evaluated.
-! Could generate 2 numbers for almost the same price, but for
-! backward compatibility generate just 1.
-!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+!> @author Cyrus Umrigar
+!>
+!> Generate a gaussian random number using Box-Mueller method.
+!> Rewrote inline function as a function so that there would be no ambiquity as to
+!> the order in which the 2 rannyu's are evaluated.
+!> Could generate 2 numbers for almost the same price, but for
+!> backward compatibility generate just 1.
       use constants, only: pi
       use precision_kinds, only: dp
       use random_mod, only: random_dp

diff --git a/src/vmc/get_norbterm.f90 b/src/vmc/get_norbterm.f90
@@ -1,3 +1,4 @@
+!> Module that computes the number of orbital parameters needed for the allocations of the arrays.
 module get_norbterm_mod
 contains
 subroutine get_norbterm

diff --git a/src/vmc/hpsi.f90 b/src/vmc/hpsi.f90
@@ -1,9 +1,14 @@
 module hpsi_mod
 contains
       subroutine hpsi(coord,psid,psij,ekin,energy,ipass,ifr)
-
-! Written by Cyrus Umrigar, modified by Claudia Filippi and A. Scemama
-! modified by Claudio Amovilli and Franca Floris for PCM and QM-MMPOl
+!> @author Cyrus Umrigar
+!> @author Claudia Filippi
+!> @author Anthony Scemama
+!> @author Claudio Amovilli
+!> @author Franca Floris
+!>
+!> Written by Cyrus Umrigar, modified by Claudia Filippi and A. Scemama
+!> modified by Claudio Amovilli and Franca Floris for PCM and QM-MMPOl
 
       use Bloc,    only: tildem,tildemkin,b,bkin
       use casula,  only: i_vpsp,t_vpsp