Add phagen version 2.3 support.

src/msspec/parameters.py

@@ -19,7 +19,7 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/parameters.py
-# Last modified: Thu, 13 Mar 2025 11:20:31 +0100
+# Last modified: Tue, 29 Apr 2025 11:49:20 +0200
 # Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes.fr>
 
 
@@ -362,8 +362,8 @@ class PhagenParameters(BaseParameters):
             Parameter('l2h', types=(int,), fmt='d', default=4),
 
             Parameter('ionicity', types=dict, default={}),
-            Parameter('noproto', allowed_values=('.true.', '.false.'),
+            #Parameter('noproto', allowed_values=('.true.', '.false.'),
-                      types=(str,), fmt='>7s', default='.true.'),
+            #          types=(str,), fmt='>7s', default='.true.'),
             #Parameter('absorber', types=(int,), limits=(1, None), fmt='d', default=1),
             #Parameter('nosym', types=(str,), allowed_values=('.true.', '.false.'), fmt='s', default='.true.'),
             #Parameter('outersph', types=(str,), allowed_values=('.true.', '.false.'), fmt='s', default='.false.'),

src/msspec/phagen/fortran/msxas3.inc

@@ -1 +0,0 @@
-phagen_2.2_dp/msxas3.inc

src/msspec/phagen/fortran/msxas3.inc

@@ -0,0 +1,74 @@
+c..   dimensions for the program
+      integer     ua_
+      parameter ( nat_     =       100,
+     $            ua_      =       100,
+     $            neq_     =        48,
+     $            thrs     =  -0.001d0  )
+C
+C   where :
+c
+c   nat_          maximum number of atoms expected in any
+c                molecule of interest (including an outer
+c                sphere. an even number is suggested).
+c
+c   ua_           maximum number of nda's (unique, or
+c                symmetry-distinct atoms) expected in any
+c                molecule (including an outer sphere).
+c
+c   neq_          maximum number of atoms expected in
+c                any symmetry-equivalent set (including
+c                the nda of the set)
+c
+c   thrs         threshold within which atoms with the same 
+c		     atomic number are considered equivalent.
+c		     If negative, all atoms are considered prototypical.
+c
+c	     Warning: This version of msxas3.inc with program
+c				phagen_scf_2.3_dp.f
+c
+c...................................................................
+c            dimensioning cont and cont_sub source program 
+c...................................................................
+c
+      integer fl_, rdx_
+c
+      parameter ( rdx_     =  1600,
+     $            lmax_    =  50,
+     $            npss     =  lmax_ + 2,
+     $            fl_       =  2*npss + 1,
+     $            nef_     =  10,
+     $            lexp_    =  10,
+     $            nep_     =  500  )
+c
+c   where :
+c
+c   rdx_          number of points of the linear-log mesh
+c
+c   lmax_         the maximum l-value used on any sphere 
+c                 (suggested value 5 or less if running valence dos section of 
+c                  phagen, 60 when calculating atomic t_l)
+c
+c   nef_          effective number of atoms used in the transition 
+c                 matrix elements of eels. Put = 1 if not doing a eels 
+c                 calculation (suggested value 12)
+c
+c   lexp_         lmax in the expansion of coulomb interaction plus one! temporary
+c
+c   nep_           the maximum number of energy points for which phase
+c                  shifts will be computed.
+c
+c.......................................................................
+c           multiple scattering paths, xn programs dimensioning
+c.......................................................................
+c
+c
+      parameter (natoms=nat_)
+c
+c
+c    where:
+c
+c      natoms  = number of centers in the system
+c
+c
+c...................................................................
+

src/msspec/phagen/fortran/msxasc3.inc

@@ -1 +0,0 @@
-phagen_2.2_dp/msxasc3.inc

src/msspec/phagen/fortran/msxasc3.inc

@@ -0,0 +1,27 @@
+      logical vinput, nosym, tdl
+      character*5 potype
+      character*1 optrsh
+      character*2 edge,charelx,edge1,edge2,potgen,relc
+      character*3 calctype,expmode,eikappr,enunit
+      character*4 coor
+      character*6 norman
+      character*7 ionzst
+      integer absorber,hole,l2h,hole1,hole2
+      dimension nz(natoms)
+      dimension c(natoms,3), rad(natoms), redf(natoms)
+      dimension neqat(natoms)
+      dimension nk0(0:lmax_)
+c.....Warning: when reordering common/options/, reorder also the same common in 
+c.....subroutine inpot
+      common/options/rsh,ovlpfac,vc0,rs0,vinput,absorber,hole,mode,
+     &      ionzst,potype,norman,coor,charelx,edge,potgen,lmax_mode,
+     &      lmaxt,relc,eikappr,optrsh,nosym,tdl   
+      common/atoms/c,rad,redf,charge_ion(100),nat,nz,neqat
+c      common/azimuth/lin,lmax
+      common/auger/calctype,expmode,edge1,edge2
+      common/auger1/lin1,lin2,hole1,hole2,l2h
+      common/funit/idat,iwr,iphas,iedl0,iwf
+      common/constant/antoau,ev,pi,pi4,pif,zero,thresh,nk0
+c....................................................................
+c rpot = if real potential is to be used
+c.....................................................................

src/msspec/phagen/fortran/msxast3.inc

@@ -0,0 +1,74 @@
+c..   dimensions for the program
+      integer     ua_
+      parameter ( nat_     =       100,
+     $            ua_      =       100,
+     $            neq_     =        48,
+     $            thrs     =  -0.001d0  )
+C
+C   where :
+c
+c   nat_          maximum number of atoms expected in any
+c                molecule of interest (including an outer
+c                sphere. an even number is suggested).
+c
+c   ua_           maximum number of nda's (unique, or
+c                symmetry-distinct atoms) expected in any
+c                molecule (including an outer sphere).
+c
+c   neq_          maximum number of atoms expected in
+c                any symmetry-equivalent set (including
+c                the nda of the set)
+c
+c   thrs         threshold within which atoms with the same 
+c		     atomic number are considered equivalent.
+c		     If negative, all atoms are considered prototypical.
+c
+c	     Warning: This version of msxas3.inc with program
+c				phagen_scf_2.3_dp.f
+c
+c...................................................................
+c            dimensioning cont and cont_sub source program 
+c...................................................................
+c
+      integer fl_, rdx_
+c
+      parameter ( rdx_     =  1600,
+     $            lmax_    =  50,
+     $            npss     =  lmax_ + 2,
+     $            fl_       =  2*npss + 1,
+     $            nef_     =  10,
+     $            lexp_    =  10,
+     $            nep_     =  500  )
+c
+c   where :
+c
+c   rdx_          number of points of the linear-log mesh
+c
+c   lmax_         the maximum l-value used on any sphere 
+c                 (suggested value 5 or less if running valence dos section of 
+c                  phagen, 60 when calculating atomic t_l)
+c
+c   nef_          effective number of atoms used in the transition 
+c                 matrix elements of eels. Put = 1 if not doing a eels 
+c                 calculation (suggested value 12)
+c
+c   lexp_         lmax in the expansion of coulomb interaction plus one! temporary
+c
+c   nep_           the maximum number of energy points for which phase
+c                  shifts will be computed.
+c
+c.......................................................................
+c           multiple scattering paths, xn programs dimensioning
+c.......................................................................
+c
+c
+      parameter (natoms=nat_)
+c
+c
+c    where:
+c
+c      natoms  = number of centers in the system
+c
+c
+c...................................................................
+

src/msspec/phagen/fortran/phagen_2.3_dp/phagen_scf_2.3_dp.f

@@ -1,5 +1,9 @@
 C
-      PROGRAM PHAGEN
+CST   ==> Phagen to python shared object modifications
+CST   Phagen becomes a subroutine in a library
+CST      PROGRAM PHAGEN
+      subroutine phagen()
+CST   Phagen to python shared object modifications <==
 C
 C  ....................................
 C  ..                                ..
@@ -148,6 +152,14 @@ C
 C... Starting to write in the check file IWR
 C      
       WRITE(IWR,1000)
+CST   ==> Phagen to python shared object modifications
+CST   Create output folders and open input file
+      CALL SYSTEM('mkdir -p div/wf')
+      CALL SYSTEM('mkdir -p plot')
+      CALL SYSTEM('mkdir -p tl')
+      CALL SYSTEM('mkdir -p clus')
+      OPEN(idat, FILE='../input/input.ms', STATUS='old')
+CST   Phagen to python shared object modifications <==
 C
 C... Opening the Fortran files
 C
@@ -301,6 +313,10 @@ C
       CLOSE(46)
       CLOSE(IWF)
       CLOSE(IPHAS)
+CST   ==> Phagen to python shared object modifications <==
+CST   explicitely close fort.55
+      CLOSE(55)
+CST   Phagen to python shared object modifications <==
 C
 C   Formats:
 C
@@ -329,6 +345,7 @@ C
       complex*16 eelsme,p1,p2,p3,ramfsr1,ramfsr2,ramfsr3
       complex*16 p3irreg,p2irreg
 C
+C
 C.....................................................................
 C
       common /continuum/ emin,emax,delta,cip,gamma,eftri,iexcpot,db
@@ -1089,7 +1106,11 @@ c
 c.....Write out atomic coordinates in symmetry-program order:
 c     each prototypical atom is followed by its sym-equivalent atoms
 c
-c      open (10,file='clus/clus.out',status='unknown')
+CST   ==> Phagen to python shared object modifications
+CST   The clus.out file needs to be opened, so I uncommented the 
+CSR   line below
+      open (10,file='clus/clus.out',status='unknown')
+CST   Phagen to python shared object modifications <==
       if( coor.eq.'au  ') then
          ipha=1
          coef=1.d0
@@ -1098,7 +1119,10 @@ c      open (10,file='clus/clus.out',status='unknown')
         ipha=2
         coef=0.529177d0
       endif
-c      write(10,888) ipha
+CST   ==> Phagen to python shared object modifications <==
+CST   I uncommented the line below
+      write(10,888) ipha
+CST   Phagen to python shared object modifications <==
   888 format(30x,i1)
       write(7,10) (neqat(i),i=1,nat)
    10 format (/,16i5,//)
@@ -1116,14 +1140,21 @@ c
              no = no + 1
              write(7,20) no,nsymbl(k),nzeq(k),xv(k)-x0,
      &                   yv(k)-y0,zv(k)-z0,neqat(k-1)
-             write(7,20) no,nsymbl(k),nzeq(k),(xv(k)-x0)*coef,
+CST   ==> Phagen to python shared object modifications
+CST   I changed the unit to 10
+CST             write(7,20) no,nsymbl(k),nzeq(k),(xv(k)-x0)*coef,
+CST     &                   (yv(k)-y0)*coef,(zv(k)-z0)*coef,neqat(k-1)
+             write(10,20) no,nsymbl(k),nzeq(k),(xv(k)-x0)*coef,
      &                   (yv(k)-y0)*coef,(zv(k)-z0)*coef,neqat(k-1)
           endif
           continue
         enddo
       enddo
 c
-c      close(10)
+CST   ==> Phagen to python shared object modifications
+CST   I uncommented the line below
+      close(10)
+CST   Phagen to python shared object modifications <==
 c
    20 format (i5,6x,a4,i5,3f10.4,i5)
 c
@@ -1667,9 +1698,10 @@ c
       common/transform/trans
       logical shift_cc
 c
-c      data zero,thrs/0.0d0,-0.001d0/ !if thrs is negative, all cluster atoms 
+CST   ==> Phagen to python shared object modifications
-c	 are considered prototypical
+CST   data zero,thrs/0.0d0,0.001d0/ !if thrs is negative, all cluster atoms are considered prototypical 
       data zero/0.0d0/
+CST   Phagen to python shared object modifications <==
 c
       data jtape/21/
       data lunout/7/
@@ -2137,7 +2169,10 @@ c     dgc contains large component radial functions
 c     common /deux/ dvn(251), dvf(251), d(251), dc(251), dgc(251,30)
 c     passc and rho0 contain 4*pi*r^2*rho(r)
 c
-      dimension r(mp),r_hs(440),rho0_hs(440)
+CST   ==> Phagen to python shared object modifications
+CST      dimension r(mp),r_hs(440),rho0_hs(440)
+      dimension r(mp),r_hs(*),rho0_hs(*)
+CST   Phagen to python shared object modifications <==
 C
       dimension dum1(mp), dum2(mp)
       dimension vcoul(mp), rho0(mp), enp(ms)
@@ -3325,6 +3360,11 @@ C
  5004    FORMAT(8(I5,1X,F7.2))
          WRITE(6,5003)
          WRITE(6,*)
+      ELSE
+         WRITE(6,5003)
+         WRITE(6,*) ' External radii read in as: '
+         WRITE(6,*) ' i    rs(i)   i=1,natoms      '
+         WRITE(6,5004) (I, RS(I), I=1,NATOMSM) 
       END IF
       IF(NWR1.NE.'  PCH') GO TO 999
       WRITE(7,*)
@@ -7548,7 +7588,14 @@ c.....this subroutine calculates the radial matrix elements
 c.....necessary for eels cross-section 
 c.....using a linear-log mesh
 c
-      common/mtxele/ nstart,nlast
+CST   ==> Phagen to Python shared object modifications
+CST   I replaced the line below
+CST   common/mtxele/ nstart,nlast
+      common/mtxele/ nstart,nlast,dmx(2),dmx1(2),qmx(3),qmx1(3),
+     $               dxdir,dxexc,nfis,nfis1,nfis2
+      real*8 nfis,nfis2,nfis1
+      complex*16 dmx,dmx1,qmx,qmx1,dxdir,dxexc
+CST   Phagen to Python shared object modifications <==
 c
       common/mtxelex/ dmxx(2),dmxx1(2),dmxxa(2),dmxxa1(2),
      &                qmxx(3),qmxx1(3),qmxxa(3),qmxxa1(3),
@@ -16871,7 +16918,14 @@ c.....(i=1,2) for lfin=l0i-1 (i=1) and lfin=l0i+1 (i=2) both for
 c.....the regular (dmxx) and irregular solution (dmxx1) using a 
 c.....linear-log mesh
 c
-      common/mtxele/ nstart,nlast
+CST   ==> Phagen to Python shared object modifications
+CST   I replaced the line below
+CST   common/mtxele/ nstart,nlast
+      common/mtxele/ nstart,nlast,dmx(2),dmx1(2),qmx(3),qmx1(3),
+     $               dxdir,dxexc,nfis,nfis1,nfis2
+      real*8 nfis,nfis2,nfis1
+      complex*16 dmx,dmx1,qmx,qmx1,dxdir,dxexc
+CST   Phagen to Python shared object modifications <==
 c
       common/mtxelex/ dmxx(2),dmxx1(2),dmxxa(2),dmxxa1(2),
      &                qmxx(3),qmxx1(3),qmxxa(3),qmxxa1(3),
@@ -20060,7 +20114,11 @@ C     MARK 12 RELEASE. NAG COPYRIGHT 1986.
 C     MARK 15 REVISED. IER-915 (APR 1991).
 C     .. Scalar Arguments ..
       INTEGER            INFO
-      CHARACTER*13       SRNAME
+CST   ==> Phagen to Python shared object modifications
+CST   I changed the dimension to automatic
+CST      CHARACTER*13       SRNAME
+      CHARACTER(*)       SRNAME
+CST   Phagen to Python shared object modifications <==
 C     ..
 C
 C  Purpose

src/msspec/phagen/fortran/phagen_scf.f

@@ -1 +0,0 @@
-phagen_2.2_dp/phagen_scf_2.2_dp.f