TREX/fparser
1
0
Fork 0
mirror of https://github.com/TREX-CoE/fparser.git synced 2024-10-02 06:21:08 +02:00
Code Issues Projects Releases Wiki Activity

creating minimal example for the demonstration

Browse Source
This commit is contained in:
Ravindra Shinde 2021-03-25 12:31:06 +01:00
parent 195b4b89a5
commit 155526d1f0
7 changed files with 206 additions and 44 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

157
src/README.md Normal file
View File

@ -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

6
src/build.sh
View File

@ -1,5 +1,5 @@
#!/bin/bash
ifort -c periodic_table_m.F90
ifort -c keywords_m.F90
ifort -c m_periodic_table.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

31
src/iochamp.f90
View File

@ -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 :: beginning, ending
character(len=72) :: fname, axis, status, filename, fmt
logical :: doit, debug
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) :: int_format = '(A, T20, I8)'
character(len=80) :: string_format = '(A, T40, A)'
character(len=20) :: real_format = '(A, T20, F14.8)'
character(len=20) :: int_format = '(A, T20, I8)'
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

0
src/keywords_m.F90 → src/m_keywords.F90
View File

0
src/periodic_table_m.F90 → src/m_periodic_table.F90
View File

11
src/test-champ.inp
View File

@ -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 molecule benzene.xyz
load determinants TZ_1M_500.det
#%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

45
src/test-champ.out
View File

@ -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
some optional comment or a blank line
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
24
molecule 1,3,7-Trimethylpurine-2,6-dione
N 1.5808 0.7027 -0.2279
C 1.7062 -0.7374 -0.2126
N 0.5340 -1.5671 -0.3503
C 0.3231 1.3600 0.0274
C -0.8123 0.4553 0.0817
C -0.6967 -0.9322 -0.0662
N -2.1886 0.6990 0.2783
C -2.8512 -0.5205 0.2532
N -1.9537 -1.5188 0.0426
C 0.6568 -3.0274 -0.1675
O 2.8136 -1.2558 -0.1693
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 F
#:defined? determinants T