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creating minimal example for the demonstration
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Ravindra Shinde
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src/README.md
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src/README.md
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# Documentation for using the modern fortran parser
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<!-- Thanks for visiting [The Markdown Guide](https://www.markdownguide.org)!
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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). -->
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## Get the code
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The parser uses a modified libfdf library. This is included in this repository as a submodule. To clone the project, do
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`git clone --recurse-submodules https://github.com/TREX-CoE/iof08.git`
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## Compilation
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## Integrate parser in your code
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### Features of the parser (including inheritance from libfdf)
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- Include another input file for parser to read using:
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` %include global.inp`
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- Include a data file for parser to read using:
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` load label filename`
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Here, depending upon the label, parser will provide the filename. For example,
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` load basis cc-pvtz.gbs`
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- Read molecular coordinates directly from the input file using
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```perl
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%block molecule
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12
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#benzene comment
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C 0.00000 1.40272 0
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H 0.00000 2.49029 0
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C -1.21479 0.70136 0
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H -2.15666 1.24515 0
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C -1.21479 -0.70136 0
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H -2.15666 -1.24515 0
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C 0.00000 -1.40272 0
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H 0.00000 -2.49029 0
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C 1.21479 -0.70136 0
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H 2.15666 -1.24515 0
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C 1.21479 0.70136 0
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H 2.15666 1.24515 0
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%endblock
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```
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- Read molecular coordinates from an external .xyz file using
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` %block molecule < caffeine.xyz `
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- Group certain keywords using the %module construct
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```perl
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%module DMC
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tau = 0.04
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etrial = -15 Ha
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%endmodule
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```
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**bold text**
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### Italic
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*italicized text*
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### Blockquote
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> blockquote
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### Ordered List
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1. First item
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2. Second item
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3. Third item
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### Unordered List
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- First item
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- Second item
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- Third item
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### Code
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`code`
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### Horizontal Rule
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---
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### Link
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[title](https://www.example.com)
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### Image
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## Extended Syntax
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These elements extend the basic syntax by adding additional features. Not all Markdown applications support these elements.
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### Table
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| Syntax | Description |
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| ----------- | ----------- |
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| Header | Title |
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| Paragraph | Text |
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### Fenced Code Block
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```
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{
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"firstName": "John",
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"lastName": "Smith",
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"age": 25
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}
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```
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### Footnote
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Here's a sentence with a footnote. [^1]
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[^1]: This is the footnote.
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### Heading ID
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### My Great Heading {#custom-id}
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### Definition List
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term
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: definition
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### Strikethrough
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~~The world is flat.~~
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### Task List
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- [x] Write the press release
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- [ ] Update the website
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- [ ] Contact the media
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@ -1,5 +1,5 @@
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#!/bin/bash
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ifort -c periodic_table_m.F90
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ifort -c keywords_m.F90
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ifort -c m_periodic_table.F90
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ifort -c m_keywords.F90
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ifort iochamp.f90 keywords_m.o periodic_table_m.o /usr/local/lib/libfdf.a
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ifort iochamp.f90 m_keywords.o m_periodic_table.o /usr/local/lib/libfdf.a
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@ -4,9 +4,6 @@
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PROGRAM iochamp
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USE fdf
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USE prec
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USE parse
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USE io_fdf
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USE utils
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! Note the following two modules are being used to store and process the parsed data
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@ -16,26 +13,23 @@ PROGRAM iochamp
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implicit none
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!--------------------------------------------------------------- Local Variables
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integer, parameter :: maxa = 100
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logical :: doit, debug, check, val, logic(10)
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logical :: beginning, ending
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character(len=72) :: fname, axis, status, filename, fmt
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logical :: doit, debug
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character(len=72) :: fname, filename, fmt
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character(len=72) :: molecule_name, key, comment
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character(2) :: symbol(maxa)
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character(len=20) :: chunks(10), subblock(10)
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character(len=30) :: keyword(5)
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integer(sp) :: i, j, ia, na, external_entry, number_of_atoms, ind
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integer(sp) :: i, j, ia, na, number_of_atoms
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integer(sp) :: isa(maxa)
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real(dp) :: coeff(maxa)
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real(sp) :: wmix
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real(dp) :: cutoff, phonon_energy, factor
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real(dp) :: phonon_energy
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real(dp) :: xa(3, maxa)
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real(dp) :: listr(maxa)
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type(block_fdf) :: bfdf, bfdf2
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type(parsed_line), pointer :: pline, pline2
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!type(fdf_file) :: fdffile
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integer :: max_iteration, max_iter, linecount, argument(5)
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real(dp) :: float_value
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character(len=1) :: char1
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character(len=20) :: real_format = '(A, T20, F14.8)'
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character(len=20) :: int_format = '(A, T20, I8)'
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character(len=80) :: string_format = '(A, T40, A)'
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@ -143,16 +137,11 @@ PROGRAM iochamp
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write(6,*) 'multiple_adiag:', multiple_adiag
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! logical :: true, .true., yes, T, and TRUE are equivalent
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debug = fdf_boolean('Debug', .TRUE.)
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write(6,'(A, L2)') 'Debug:', debug
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! ianalyt_lap 1 isc 2 nspin1 1 nspin2 1 ifock 0
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analytic_laplacian = fdf_get('ianalyt_lap', 1)
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write(6,*) 'analytic laplacian from global.fdf pointer explained ', ianalyt_lap
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@ -216,7 +205,7 @@ PROGRAM iochamp
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ia = 1
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open (unit=12,file=file_molecule, iostat=iostat, action='read' )
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if (iostat .ne. 0) call die(file_molecule, "Problem in opening the molecule file")
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if (iostat .ne. 0) stop "Problem in opening the molecule file"
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read(12,*) natoms
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print*, "natoms ", natoms
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if (.not. allocated(cent)) allocate(cent(3,natoms))
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@ -365,7 +354,7 @@ PROGRAM iochamp
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write(6,*) 'Reading the determinants block from an external file '
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open (unit=11,file=file_determinants, iostat=iostat, action='read' )
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if (iostat .ne. 0) call die(file_determinants, "Problem in opening the determinant file")
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if (iostat .ne. 0) stop "Problem in opening the determinant file"
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read(11,*) temp1, temp2, nelectrons, temp3, nalpha
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read(11,*) temp1, ndeterminants, nexcitation
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@ -8,13 +8,18 @@
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%endmodule
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# Include another input file
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%include global.inp
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# load the data files using "load"
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load basis BFD-T-normf0.bas
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#load determinants TZ_1M_500.det
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#load molecule benzene.xyz
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load determinants TZ_1M_500.det
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#%block molecule < caffeine.xyz
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# Option 1 (higher priority compared to option 2)
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%block molecule < caffeine.xyz
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# Option 2
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%block molecule
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12
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some optional comment or a blank line
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@ -3,7 +3,7 @@ pool ./pool
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molecule default.xyz # default value
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pseudopot default.psp # default value
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basis BFD-T-normf0.bas
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determinants default.det # default value
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determinants TZ_1M_500.det
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orbitals default.orb # default value
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jastrow default.jas # default value
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jastrow_deriv default.jasder # default value
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@ -34,20 +34,31 @@ excess_charge 0 # default value
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multiplicity 1 # default value
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%block molecule
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%block molecule
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12
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some optional comment or a blank line
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C 0.00000 1.40272 0
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H 0.00000 2.49029 0
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C -1.21479 0.70136 0
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H -2.15666 1.24515 0
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C -1.21479 -0.70136 0
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H -2.15666 -1.24515 0
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C 0.00000 -1.40272 0
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H 0.00000 -2.49029 0
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C 1.21479 -0.70136 0
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H 2.15666 -1.24515 0
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C 1.21479 0.70136 0
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H 2.15666 1.24515 0
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24
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molecule 1,3,7-Trimethylpurine-2,6-dione
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N 1.5808 0.7027 -0.2279
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C 1.7062 -0.7374 -0.2126
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N 0.5340 -1.5671 -0.3503
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C 0.3231 1.3600 0.0274
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C -0.8123 0.4553 0.0817
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C -0.6967 -0.9322 -0.0662
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N -2.1886 0.6990 0.2783
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C -2.8512 -0.5205 0.2532
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N -1.9537 -1.5188 0.0426
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C 0.6568 -3.0274 -0.1675
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O 2.8136 -1.2558 -0.1693
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O 0.2849 2.5744 0.1591
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C -2.8096 2.0031 0.5032
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C 2.8301 1.5004 -0.1968
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H -3.9271 -0.6787 0.3762
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H 1.4823 -3.4046 -0.7865
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H -0.2708 -3.5204 -0.4868
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H 0.8567 -3.2990 0.8788
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H -2.4123 2.7478 -0.2017
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H -2.6042 2.3621 1.5221
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H -3.8973 1.9344 0.3695
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H 3.5959 1.0333 -0.8314
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H 3.2249 1.5791 0.8255
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H 2.6431 2.5130 -0.5793
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%endblock molecule
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#:block? determinants F
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#:defined? determinants F
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#:defined? determinants T
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