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creating minimal example for the demonstration

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Ravindra Shinde 2021-03-25 12:31:06 +01:00
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src/README.md Normal file
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# Documentation for using the modern fortran parser
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## 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
```
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src/build.sh
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#!/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

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src/iochamp.f90
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@ -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

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src/keywords_m.F90 → src/m_keywords.F90
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src/periodic_table_m.F90 → src/m_periodic_table.F90
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src/test-champ.inp
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%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

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src/test-champ.out
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@ -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