creating minimal example for the demonstration

src/README.md

@@ -0,0 +1,157 @@
+# Documentation for using the modern fortran parser
+
+<!-- Thanks for visiting [The Markdown Guide](https://www.markdownguide.org)!
+
+This Markdown cheat sheet provides a quick overview of all the Markdown syntax elements. It can’t cover every edge case, so if you need more information about any of these elements, refer to the reference guides for [basic syntax](https://www.markdownguide.org/basic-syntax) and [extended syntax](https://www.markdownguide.org/extended-syntax). -->
+
+## Get the code
+  The parser uses a modified libfdf library. This is included in this repository as a submodule. To clone the project, do
+
+
+  `git clone --recurse-submodules https://github.com/TREX-CoE/iof08.git`
+
+
+## Compilation
+
+
+
+## Integrate parser in your code
+
+
+
+### Features of the parser (including inheritance from libfdf)
+
+- Include another input file for parser to read using:
+
+` %include    global.inp`
+
+- Include a data file for parser to read using:
+
+` load label filename`
+
+Here, depending upon the label, parser will provide the filename. For example,
+
+` load basis cc-pvtz.gbs`
+
+- Read molecular coordinates directly from the input file using 
+
+```perl
+%block molecule 
+12
+ #benzene comment
+ C    0.00000    1.40272  0
+ H    0.00000    2.49029  0
+ C   -1.21479    0.70136  0
+ H   -2.15666    1.24515  0
+ C   -1.21479   -0.70136  0
+ H   -2.15666   -1.24515  0
+ C    0.00000   -1.40272  0
+ H    0.00000   -2.49029  0
+ C    1.21479   -0.70136  0
+ H    2.15666   -1.24515  0
+ C    1.21479    0.70136  0
+ H    2.15666    1.24515  0
+%endblock
+```
+
+- Read molecular coordinates from an external .xyz file using 
+
+` %block molecule < caffeine.xyz `
+
+
+- Group certain keywords using the %module construct
+
+```perl
+%module DMC
+    tau     =   0.04
+    etrial  = -15 Ha
+%endmodule
+```
+
+
+
+
+
+**bold text**
+
+### Italic
+
+*italicized text*
+
+### Blockquote
+
+> blockquote
+
+### Ordered List
+
+1. First item
+2. Second item
+3. Third item
+
+### Unordered List
+
+- First item
+- Second item
+- Third item
+
+### Code
+
+`code`
+
+### Horizontal Rule
+
+---
+
+### Link
+
+[title](https://www.example.com)
+
+### Image
+
+![alt text](image.jpg)
+
+## Extended Syntax
+
+These elements extend the basic syntax by adding additional features. Not all Markdown applications support these elements.
+
+### Table
+
+| Syntax | Description |
+| ----------- | ----------- |
+| Header | Title |
+| Paragraph | Text |
+
+### Fenced Code Block
+
+```
+{
+  "firstName": "John",
+  "lastName": "Smith",
+  "age": 25
+}
+```
+
+### Footnote
+
+Here's a sentence with a footnote. [^1]
+
+[^1]: This is the footnote.
+
+### Heading ID
+
+### My Great Heading {#custom-id}
+
+### Definition List
+
+term
+: definition
+
+### Strikethrough
+
+~~The world is flat.~~
+
+### Task List
+
+- [x] Write the press release
+- [ ] Update the website
+- [ ] Contact the media

src/build.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-ifort -c periodic_table_m.F90
+ifort -c m_periodic_table.F90
-ifort -c keywords_m.F90
+ifort -c m_keywords.F90
 
-ifort iochamp.f90 keywords_m.o periodic_table_m.o /usr/local/lib/libfdf.a
+ifort iochamp.f90 m_keywords.o m_periodic_table.o /usr/local/lib/libfdf.a

src/iochamp.f90

@@ -4,9 +4,6 @@
 PROGRAM iochamp
   USE fdf
   USE prec
-  USE parse
-  USE io_fdf
-  USE utils
 
 
 ! Note the following two modules are being used to store and process the parsed data  
@@ -16,29 +13,26 @@ PROGRAM iochamp
   implicit none
 !--------------------------------------------------------------- Local Variables
   integer, parameter         :: maxa = 100
-  logical                    :: doit, debug, check, val, logic(10)
+  logical                    :: doit, debug
-  logical                    :: beginning, ending
+
-  character(len=72)          :: fname, axis, status, filename, fmt
+  character(len=72)          :: fname, filename, fmt
   character(len=72)          :: molecule_name, key, comment
   character(2)               :: symbol(maxa)
   character(len=20)          :: chunks(10), subblock(10)
   character(len=30)          :: keyword(5) 
-  integer(sp)                :: i, j, ia, na, external_entry, number_of_atoms, ind
+  integer(sp)                :: i, j, ia, na, number_of_atoms
   integer(sp)                :: isa(maxa)
   real(dp)                   :: coeff(maxa)
   real(sp)                   :: wmix
-  real(dp)                   :: cutoff, phonon_energy, factor
+  real(dp)                   :: phonon_energy
   real(dp)                   :: xa(3, maxa)
   real(dp)                   :: listr(maxa)
   type(block_fdf)            :: bfdf, bfdf2
   type(parsed_line), pointer :: pline, pline2
-  !type(fdf_file)             :: fdffile 
-  integer                    ::  max_iteration, max_iter, linecount, argument(5)
   real(dp)                   :: float_value
-  character(len=1)           :: char1
+  character(len=20)          :: real_format    = '(A, T20, F14.8)'
-  character(len=20)          :: real_format = '(A, T20, F14.8)'
+  character(len=20)          :: int_format     = '(A, T20, I8)'
-  character(len=20)          :: int_format = '(A, T20, I8)'
+  character(len=80)          :: string_format  = '(A, T40, A)'  
-  character(len=80)          :: string_format = '(A, T40, A)'  
 
 ! for determinants sections
   integer                    :: nelectrons, nexcitation, iostat
@@ -143,16 +137,11 @@ PROGRAM iochamp
   write(6,*) 'multiple_adiag:', multiple_adiag
 
 
-
-
-
   ! logical :: true, .true., yes, T, and TRUE are equivalent
   debug = fdf_boolean('Debug', .TRUE.)
   write(6,'(A, L2)') 'Debug:', debug
 
 
-
-
 ! ianalyt_lap 1 isc 2 nspin1 1 nspin2 1 ifock 0
   analytic_laplacian = fdf_get('ianalyt_lap', 1)
   write(6,*) 'analytic laplacian from global.fdf pointer explained ', ianalyt_lap
@@ -216,7 +205,7 @@ PROGRAM iochamp
           ia = 1
 
           open (unit=12,file=file_molecule, iostat=iostat, action='read' )
-          if (iostat .ne. 0) call die(file_molecule, "Problem in opening the molecule file")          
+          if (iostat .ne. 0) stop "Problem in opening the molecule file"
           read(12,*) natoms
           print*, "natoms ", natoms
           if (.not. allocated(cent)) allocate(cent(3,natoms))
@@ -365,7 +354,7 @@ PROGRAM iochamp
         write(6,*) 'Reading the determinants block from an external file '
 
         open (unit=11,file=file_determinants, iostat=iostat, action='read' )
-        if (iostat .ne. 0) call die(file_determinants, "Problem in opening the determinant file")
+        if (iostat .ne. 0) stop "Problem in opening the determinant file"
         read(11,*) temp1, temp2, nelectrons, temp3, nalpha
 
         read(11,*)  temp1, ndeterminants, nexcitation

src/test-champ.inp

@@ -8,13 +8,18 @@
 
 %endmodule
 
+# Include another input file 
 %include            global.inp
+
+# load the data files using "load" 
 load basis          BFD-T-normf0.bas
-#load determinants   TZ_1M_500.det
+load determinants   TZ_1M_500.det
-#load molecule  benzene.xyz
 
-#%block molecule < caffeine.xyz
+# Option 1 (higher priority compared to option 2)
+%block molecule < caffeine.xyz
 
+
+# Option 2
 %block molecule 
 12
 some optional comment or a blank line

src/test-champ.out

@@ -3,7 +3,7 @@ pool     ./pool
 molecule     default.xyz     # default value
 pseudopot     default.psp     # default value
 basis     BFD-T-normf0.bas                                                                
-determinants     default.det     # default value
+determinants     TZ_1M_500.det                                                                   
 orbitals     default.orb     # default value
 jastrow     default.jas     # default value
 jastrow_deriv     default.jasder     # default value
@@ -34,20 +34,31 @@ excess_charge         0     # default value
 multiplicity         1     # default value
 %block molecule
 %block molecule
- 12
+ 24
- some optional comment or a blank line
+ molecule 1,3,7-Trimethylpurine-2,6-dione
-  C    0.00000    1.40272  0
+   N      1.5808      0.7027     -0.2279
-  H    0.00000    2.49029  0
+   C      1.7062     -0.7374     -0.2126
-  C   -1.21479    0.70136  0
+   N      0.5340     -1.5671     -0.3503
-  H   -2.15666    1.24515  0
+   C      0.3231      1.3600      0.0274
-  C   -1.21479   -0.70136  0
+   C     -0.8123      0.4553      0.0817
-  H   -2.15666   -1.24515  0
+   C     -0.6967     -0.9322     -0.0662
-  C    0.00000   -1.40272  0
+   N     -2.1886      0.6990      0.2783
-  H    0.00000   -2.49029  0
+   C     -2.8512     -0.5205      0.2532
-  C    1.21479   -0.70136  0
+   N     -1.9537     -1.5188      0.0426
-  H    2.15666   -1.24515  0
+   C      0.6568     -3.0274     -0.1675
-  C    1.21479    0.70136  0
+   O      2.8136     -1.2558     -0.1693
-  H    2.15666    1.24515  0
+   O      0.2849      2.5744      0.1591
+   C     -2.8096      2.0031      0.5032
+   C      2.8301      1.5004     -0.1968
+   H     -3.9271     -0.6787      0.3762
+   H      1.4823     -3.4046     -0.7865
+   H     -0.2708     -3.5204     -0.4868
+   H      0.8567     -3.2990      0.8788
+   H     -2.4123      2.7478     -0.2017
+   H     -2.6042      2.3621      1.5221
+   H     -3.8973      1.9344      0.3695
+   H      3.5959      1.0333     -0.8314
+   H      3.2249      1.5791      0.8255
+   H      2.6431      2.5130     -0.5793
 %endblock molecule
-#:block? determinants              F
+#:defined? determinants              T
-#:defined? determinants              F