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Merge branch 'master' into add-python-api

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q-posev 2022-05-02 17:11:11 +02:00
commit bfbdfa3b76
14 changed files with 1296 additions and 531 deletions
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44
.github/workflows/test-build.yml vendored
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@ -47,6 +47,7 @@ jobs:
- name: Run test
run: make -j 4 check
working-directory: _build
- name: Archive test log file
if: failure()
@ -57,13 +58,7 @@ jobs:
- name: Dist test
run: make distcheck
- name: Archive test log file
if: failure()
uses: actions/upload-artifact@v2
with:
name: dist-report-ubuntu
path: test-suite.log
working-directory: _build
x86_macos:
@ -91,37 +86,26 @@ jobs:
git clone https://github.com/TREX-CoE/trexio.git
cd trexio
./autogen.sh
mkdir _build
cd _build
../configure --enable-silent-rules
make -j 4
- name: Run test
run: make -j 4 check
- name: Archive test log file
if: failure()
uses: actions/upload-artifact@v2
with:
name: test-report-ubuntu
path: test-suite.log
- name: Dist test
run: make distcheck
- name: Archive test log file
if: failure()
uses: actions/upload-artifact@v2
with:
./configure --prefix=${PWD}/_install --enable-silent-rules
make -j 4
make install
- name: Test TREXIO
run: make -j 4 check
working-directory: trexio
- name: Archive TREXIO test log file
if: failure()
uses: actions/upload-artifact@v2
with:
name: test-report-trexio-macos
path: trexio/test-suite.log
- name: Build QMCkl
run: |
export PKG_CONFIG_PATH=${PWD}/trexio/_install/lib/pkgconfig:$PKG_CONFIG_PATH
./autogen.sh
./configure --enable-silent-rules --enable-debug
./configure CC=gcc-10 FC=gfortran-10 --enable-silent-rules --enable-debug
make -j 4
- name: Run test

18
README.md
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@ -73,6 +73,24 @@ sudo make install
sudo make installcheck
```
## Linking to your program
The `make install` command takes care of installing the QMCkl shared library on the user machine.
Once installed, add `-lqmckl` to the list of compiler options.
In some cases (e.g. when using custom `prefix` during configuration), the QMCkl library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
In order to link the program against QMCkl, the search paths can be modified as follows:
`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_qmckl>/lib`
(same holds for `$LD_LIBRARY_PATH`). The `<path_to_qmckl>` has to be replaced with the prefix used during the installation.
If your project relies on the CMake build system, feel free to use the
[FindQMCKL.cmake](https://github.com/TREX-CoE/qmckl/blob/master/cmake/FindQMCKL.cmake)
module to find and link the QMCkl library automatically.
## Verificarlo CI
Since Verificarlo should not be a dependency of QMCkl, all Verificarlo

77
cmake/FindQMCKL.cmake Normal file
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@ -0,0 +1,77 @@
#===========================================
# Try to find the QMCkl library;
# If found, it will define the following variables (note the plural form):
# QMCKL_FOUND - System has libqmckl;
# QMCKL_INCLUDE_DIRS - The QMCKL include directories;
# QMCKL_LIBRARIES - The libraries needed to use QMCKL;
# If QMCKL has been installed in a non-standard location, one can set an
# environment variable $QMCKL_DIR in the current shell:
# $ export QMCKL_DIR=<custom_path>
# to indicate the prefix used during the QMCKL installation
# (typically `./configure prefix=<custom_path> ..` or `cmake -DCMAKE_INSTALL_DIR=<custom_path> ..`)
# This file should be located WITHIN your project source tree.
# (e.g. in cmake/FindQMCKL.cmake)
# How to use it in your project CMakeLists.txt:
# This is needed to locate FindQMCKL.cmake file, modify it according to your source tree.
# list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/")
# find_package(QMCKL)
# if (QMCKL_FOUND)
# include_directories(${QMCKL_INCLUDE_DIRS})
# target_link_libraries(your_target ${QMCKL_LIBRARIES})
# endif()
#===========================================
# This file is distirbuted under the BSD 3-Clause License.
# Copyright (c) 2021, TREX Center of Excellence
#===========================================
message("<FindQMCKL.cmake>")
set(QMCKL_SEARCH_PATHS
~/Library/Frameworks
/Library/Frameworks
/usr/local
/usr
/sw # Fink
/opt/local # DarwinPorts
/opt/csw # Blastwave
/opt
)
find_path(QMCKL_INCLUDE_DIR
NAMES qmckl.h
HINTS $ENV{QMCKL_DIR}
PATH_SUFFIXES include/qmckl include
PATHS ${QMCKL_SEARCH_PATHS}
)
# No need to specify platform-specific prefix (e.g. libqmckl on Unix) or
# suffix (e.g. .so on Unix or .dylib on MacOS) in NAMES. CMake takes care of that.
find_library(QMCKL_LIBRARY
NAMES qmckl
HINTS $ENV{QMCKL_DIR}
PATH_SUFFIXES lib64 lib
PATHS ${QMCKL_SEARCH_PATHS}
)
message("<FindQMCKL.cmake>")
# Handle the QUIETLY and REQUIRED arguments and set QMCKL_FOUND to TRUE if
# all listed variables are TRUE.
INCLUDE(FindPackageHandleStandardArgs)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(QMCKL DEFAULT_MSG QMCKL_LIBRARY QMCKL_INCLUDE_DIR )
MARK_AS_ADVANCED(QMCKL_INCLUDE_DIR QMCKL_LIBRARY)
# Mot setting _INCLUDE_DIR and _LIBRARIES is considered a bug,
# see https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/How-To-Find-Libraries
set(QMCKL_LIBRARIES ${QMCKL_LIBRARY})
set(QMCKL_INCLUDE_DIRS ${QMCKL_INCLUDE_DIR})

22
configure.ac
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@ -49,12 +49,12 @@ AS_IF([test -d ${srcdir}/.git],
AC_ARG_WITH(ifort, [AS_HELP_STRING([--with-ifort],[Use Intel Fortran compiler])], with_ifort=$withval, with_ifort=no)
AS_IF([test "$with_ifort" == "yes"], [
FC=ifort
FCFLAGS="-xHost -ip -Ofast -ftz -finline -g -mkl=sequential" ])
FCFLAGS="-march=native -ip -Ofast -ftz -finline -g -mkl=sequential" ])
AC_ARG_WITH(icc, [AS_HELP_STRING([--with-icc],[Use Intel C compiler])], with_icc=$withval, with_icc=no)
AS_IF([test "$with_icc" == "yes"], [
CC=icc
CFLAGS="-xHost -ip -Ofast -ftz -finline -g -mkl=sequential" ])
CFLAGS="-march=native -ip -Ofast -ftz -finline -g -mkl=sequential" ])
AS_IF([test "$with_icc"."$with_ifort" == "yes.yes"], [
ax_blas_ok="yes"
@ -200,16 +200,22 @@ AS_IF([test "$BLAS_LIBS" == "$LAPACK_LIBS"], [BLAS_LIBS=""])
# Specific options required with some compilers
case $FC in
ifort*)
*ifort*)
FCFLAGS="$FCFLAGS -nofor-main"
;;
#gfortran*)
# # Order is important here
# FCFLAGS="-cpp $FCFLAGS"
# ;;
*nvfortran*)
FCFLAGS="$FCFLAGS -fPIC -Mnomain"
;;
esac
case $CC in
*nvc*)
CFLAGS="$CFLAGS -fPIC"
;;
esac
# Options.
@ -358,7 +364,7 @@ CC..............: ${CC}
CPPFLAGS........: ${CPPFLAGS}
CFLAGS..........: ${CFLAGS}
FC..............: ${FC}
FCLAGS..........: ${FCFLAGS}
FCFLAGS.........: ${FCFLAGS}
LDFLAGS:........: ${LDFLAGS}
LIBS............: ${LIBS}
USE CHAMELEON...: ${with_chameleon}

199
org/examples.org Normal file
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@ -0,0 +1,199 @@
#+TITLE: Code examples
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
In this section, we present examples of usage of QMCkl.
For simplicity, we assume that the wave function parameters are stores
in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
* Checking errors
All QMCkl functions return an error code. A convenient way to handle
errors is to write an error-checking function that displays the
error in text format and exits the program.
#+NAME: qmckl_check_error
#+begin_src f90
subroutine qmckl_check_error(rc, message)
use qmckl
implicit none
integer(qmckl_exit_code), intent(in) :: rc
character(len=*) , intent(in) :: message
character(len=128) :: str_buffer
if (rc /= QMCKL_SUCCESS) then
print *, message
call qmckl_string_of_error(rc, str_buffer)
print *, str_buffer
call exit(rc)
end if
end subroutine qmckl_check_error
#+end_src
* Computing an atomic orbital on a grid
:PROPERTIES:
:header-args: :tangle ao_grid.f90
:END:
The following program, in Fortran, computes the values of an atomic
orbital on a regular 3-dimensional grid. The 100^3 grid points are
automatically defined, such that the molecule fits in a box with 5
atomic units in the borders.
This program uses the ~qmckl_check_error~ function defined above.
To use this program, run
#+begin_src bash :tangle no
$ ao_grid <trexio_file> <AO_id> <point_num>
#+end_src
#+begin_src f90 :noweb yes
<<qmckl_check_error>>
program ao_grid
use qmckl
implicit none
integer(qmckl_context) :: qmckl_ctx ! QMCkl context
integer(qmckl_exit_code) :: rc ! Exit code of QMCkl functions
character(len=128) :: trexio_filename
character(len=128) :: str_buffer
integer :: ao_id
integer :: point_num_x
integer(c_int64_t) :: nucl_num
double precision, allocatable :: nucl_coord(:,:)
integer(c_int64_t) :: point_num
integer(c_int64_t) :: ao_num
integer(c_int64_t) :: ipoint, i, j, k
double precision :: x, y, z, dr(3)
double precision :: rmin(3), rmax(3)
double precision, allocatable :: points(:,:)
double precision, allocatable :: ao_vgl(:,:,:)
#+end_src
Start by fetching the command-line arguments:
#+begin_src f90
if (iargc() /= 3) then
print *, 'Syntax: ao_grid <trexio_file> <AO_id> <point_num>'
call exit(-1)
end if
call getarg(1, trexio_filename)
call getarg(2, str_buffer)
read(str_buffer, *) ao_id
call getarg(3, str_buffer)
read(str_buffer, *) point_num_x
if (point_num_x < 0 .or. point_num_x > 300) then
print *, 'Error: 0 < point_num < 300'
call exit(-1)
end if
#+end_src
Create the QMCkl context and initialize it with the wave function
present in the TREXIO file:
#+begin_src f90
qmckl_ctx = qmckl_context_create()
rc = qmckl_trexio_read(qmckl_ctx, trexio_filename, 1_8*len(trim(trexio_filename)))
call qmckl_check_error(rc, 'Read TREXIO')
#+end_src
We need to check that ~ao_id~ is in the range, so we get the total
number of AOs from QMCkl:
#+begin_src f90
rc = qmckl_get_ao_basis_ao_num(qmckl_ctx, ao_num)
call qmckl_check_error(rc, 'Getting ao_num')
if (ao_id < 0 .or. ao_id > ao_num) then
print *, 'Error: 0 < ao_id < ', ao_num
call exit(-1)
end if
#+end_src
Now we will compute the limits of the box in which the molecule fits.
For that, we first need to ask QMCkl the coordinates of nuclei.
#+begin_src f90
rc = qmckl_get_nucleus_num(qmckl_ctx, nucl_num)
call qmckl_check_error(rc, 'Get nucleus num')
allocate( nucl_coord(3, nucl_num) )
rc = qmckl_get_nucleus_coord(qmckl_ctx, 'N', nucl_coord, 3_8*nucl_num)
call qmckl_check_error(rc, 'Get nucleus coord')
#+end_src
We now compute the coordinates of opposite points of the box, and
the distance between points along the 3 directions:
#+begin_src f90
rmin(1) = minval( nucl_coord(1,:) ) - 5.d0
rmin(2) = minval( nucl_coord(2,:) ) - 5.d0
rmin(3) = minval( nucl_coord(3,:) ) - 5.d0
rmax(1) = maxval( nucl_coord(1,:) ) + 5.d0
rmax(2) = maxval( nucl_coord(2,:) ) + 5.d0
rmax(3) = maxval( nucl_coord(3,:) ) + 5.d0
dr(1:3) = (rmax(1:3) - rmin(1:3)) / dble(point_num_x-1)
#+end_src
We now produce the list of point coordinates where the AO will be
evaluated:
#+begin_src f90
point_num = point_num_x**3
allocate( points(point_num, 3) )
ipoint=0
z = rmin(3)
do k=1,point_num_x
y = rmin(2)
do j=1,point_num_x
x = rmin(1)
do i=1,point_num_x
ipoint = ipoint+1
points(ipoint,1) = x
points(ipoint,2) = y
points(ipoint,3) = z
x = x + dr(1)
end do
y = y + dr(2)
end do
z = z + dr(3)
end do
#+end_src
We give the points to QMCkl:
#+begin_src f90
rc = qmckl_set_point(qmckl_ctx, 'T', points, point_num)
call qmckl_check_error(rc, 'Setting points')
#+end_src
We allocate the space required to retrieve the values, gradients and
Laplacian of all AOs, and ask to retrieve the values of the
AOs computed at the point positions.
#+begin_src f90
allocate( ao_vgl(ao_num, 5, point_num) )
rc = qmckl_get_ao_basis_ao_vgl(qmckl_ctx, ao_vgl, ao_num*5_8*point_num)
call qmckl_check_error(rc, 'Setting points')
#+end_src
We finally print the value of the AO:
#+begin_src f90
do ipoint=1, point_num
print '(3(F16.10,X),E20.10)', points(ipoint, 1:3), ao_vgl(ao_id,1,ipoint)
end do
#+end_src
#+begin_src f90
deallocate( nucl_coord, points, ao_vgl )
end program ao_grid
#+end_src

930
org/qmckl_ao.org
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6
org/qmckl_blas.org
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@ -85,7 +85,7 @@ are not intended to be passed to external codes.
#+begin_src c :comments org :tangle (eval h_private_type) :exports none
typedef struct qmckl_vector {
int64_t size;
double* data;
double* restrict data;
} qmckl_vector;
#+end_src
@ -161,7 +161,7 @@ qmckl_vector_free( qmckl_context context,
#+begin_src c :comments org :tangle (eval h_private_type) :exports none
typedef struct qmckl_matrix {
int64_t size[2];
double* data;
double* restrict data;
} qmckl_matrix;
#+end_src
@ -247,7 +247,7 @@ qmckl_matrix_free( qmckl_context context,
typedef struct qmckl_tensor {
int64_t order;
int64_t size[QMCKL_TENSOR_ORDER_MAX];
double* data;
double* restrict data;
} qmckl_tensor;
#+end_src

16
org/qmckl_context.org
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@ -169,7 +169,7 @@ qmckl_context qmckl_context_check(const qmckl_context context) {
if (context == QMCKL_NULL_CONTEXT)
return QMCKL_NULL_CONTEXT;
const qmckl_context_struct* const ctx = (const qmckl_context_struct* const) context;
const qmckl_context_struct* const ctx = (const qmckl_context_struct*) context;
/* Try to access memory */
if (ctx->tag != VALID_TAG) {
@ -209,7 +209,7 @@ qmckl_context_touch(const qmckl_context context)
NULL);
}
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
qmckl_context_struct* const ctx = (qmckl_context_struct*) context;
ctx->date += 1UL;
ctx->point.date += 1UL;
@ -234,7 +234,7 @@ qmckl_context qmckl_context_create();
qmckl_context qmckl_context_create() {
qmckl_context_struct* const ctx =
(qmckl_context_struct* const) malloc (sizeof(qmckl_context_struct));
(qmckl_context_struct*) malloc (sizeof(qmckl_context_struct));
if (ctx == NULL) {
return QMCKL_NULL_CONTEXT;
@ -350,7 +350,7 @@ void qmckl_unlock(qmckl_context context);
void qmckl_lock(qmckl_context context) {
if (context == QMCKL_NULL_CONTEXT)
return ;
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
qmckl_context_struct* const ctx = (qmckl_context_struct*) context;
errno = 0;
int rc = pthread_mutex_lock( &(ctx->mutex) );
if (rc != 0) {
@ -362,7 +362,7 @@ void qmckl_lock(qmckl_context context) {
}
void qmckl_unlock(const qmckl_context context) {
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
qmckl_context_struct* const ctx = (qmckl_context_struct*) context;
int rc = pthread_mutex_unlock( &(ctx->mutex) );
if (rc != 0) {
fprintf(stderr, "DEBUG qmckl_unlock:%s\n", strerror(rc) );
@ -401,10 +401,10 @@ qmckl_context qmckl_context_copy(const qmckl_context context) {
{
const qmckl_context_struct* const old_ctx =
(qmckl_context_struct* const) checked_context;
(qmckl_context_struct*) checked_context;
qmckl_context_struct* const new_ctx =
(qmckl_context_struct* const) malloc (context, sizeof(qmckl_context_struct));
(qmckl_context_struct*) malloc (context, sizeof(qmckl_context_struct));
if (new_ctx == NULL) {
qmckl_unlock(context);
@ -467,7 +467,7 @@ qmckl_context_destroy (const qmckl_context context)
const qmckl_context checked_context = qmckl_context_check(context);
if (checked_context == QMCKL_NULL_CONTEXT) return QMCKL_INVALID_CONTEXT;
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
qmckl_context_struct* const ctx = (qmckl_context_struct*) context;
assert (ctx != NULL); /* Shouldn't be possible because the context is valid */
qmckl_lock(context);

8
org/qmckl_determinant.org
View File

@ -1239,9 +1239,9 @@ assert(rc == QMCKL_SUCCESS);
assert(qmckl_ao_basis_provided(context));
double ao_vgl[5][walk_num][elec_num][chbrclf_ao_num];
double ao_vgl[walk_num*elec_num][5][chbrclf_ao_num];
rc = qmckl_get_ao_basis_ao_vgl(context, &(ao_vgl[0][0][0][0]), (int64_t) 5*walk_num*elec_num*chbrclf_ao_num);
rc = qmckl_get_ao_basis_ao_vgl(context, &(ao_vgl[0][0][0]), (int64_t) 5*walk_num*elec_num*chbrclf_ao_num);
assert (rc == QMCKL_SUCCESS);
/* Set up MO data */
@ -1256,8 +1256,8 @@ assert (rc == QMCKL_SUCCESS);
assert(qmckl_mo_basis_provided(context));
double mo_vgl[5][elec_num][chbrclf_mo_num];
rc = qmckl_get_mo_basis_vgl(context, &(mo_vgl[0][0][0]));
double mo_vgl[walk_num*elec_num][5][chbrclf_mo_num];
rc = qmckl_get_mo_basis_mo_vgl(context, &(mo_vgl[0][0][0]), 5*walk_num*elec_num*chbrclf_mo_num);
assert (rc == QMCKL_SUCCESS);
/* Set up determinant data */

8
org/qmckl_local_energy.org
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@ -655,9 +655,9 @@ assert(rc == QMCKL_SUCCESS);
assert(qmckl_ao_basis_provided(context));
double ao_vgl[5][walk_num][elec_num][chbrclf_ao_num];
double ao_vgl[walk_num*elec_num][5][chbrclf_ao_num];
rc = qmckl_get_ao_basis_ao_vgl(context, &(ao_vgl[0][0][0][0]),
rc = qmckl_get_ao_basis_ao_vgl(context, &(ao_vgl[0][0][0]),
(int64_t) 5*walk_num*elec_num*chbrclf_ao_num);
assert (rc == QMCKL_SUCCESS);
@ -673,8 +673,8 @@ assert (rc == QMCKL_SUCCESS);
assert(qmckl_mo_basis_provided(context));
double mo_vgl[5][elec_num][chbrclf_mo_num];
rc = qmckl_get_mo_basis_vgl(context, &(mo_vgl[0][0][0]));
double mo_vgl[walk_num*elec_num][5][chbrclf_mo_num];
rc = qmckl_get_mo_basis_mo_vgl(context, &(mo_vgl[0][0][0]), 5*walk_num*elec_num*chbrclf_mo_num);
assert (rc == QMCKL_SUCCESS);
/* Set up determinant data */

482
org/qmckl_mo.org
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@ -84,13 +84,14 @@ int main() {
The following arrays are stored in the context:
|---------------+--------------------+----------------------|
| ~mo_num~ | | Number of MOs |
| ~coefficient~ | ~[mo_num][ao_num]~ | Orbital coefficients |
|-----------------+--------------------+----------------------------------------|
| ~mo_num~ | | Number of MOs |
| ~coefficient~ | ~[mo_num][ao_num]~ | Orbital coefficients |
| ~coefficient_t~ | ~[ao_num][mo_num]~ | Transposed of the Orbital coefficients |
|-----------------+--------------------+----------------------------------------|
Computed data:
|---------------+--------------------------+-------------------------------------------------------------------------------------|
|---------------+--------------------------+-------------------------------------------------------------------------------------|
| ~mo_vgl~ | ~[point_num][5][mo_num]~ | Value, gradients, Laplacian of the MOs at point positions |
| ~mo_vgl_date~ | ~uint64_t~ | Late modification date of Value, gradients, Laplacian of the MOs at point positions |
@ -101,9 +102,10 @@ int main() {
#+begin_src c :comments org :tangle (eval h_private_type)
typedef struct qmckl_mo_basis_struct {
int64_t mo_num;
double * coefficient;
double * restrict coefficient;
double * restrict coefficient_t;
double * mo_vgl;
double * restrict mo_vgl;
uint64_t mo_vgl_date;
int32_t uninitialized;
@ -255,6 +257,35 @@ bool qmckl_mo_basis_provided(const qmckl_context context) {
#+end_src
*** Fortran interfaces
#+begin_src f90 :tangle (eval fh_func) :comments org
interface
integer(c_int32_t) function qmckl_get_mo_basis_mo_num (context, &
mo_num) bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(out) :: mo_num
end function qmckl_get_mo_basis_mo_num
end interface
interface
integer(c_int32_t) function qmckl_get_mo_basis_coefficient(context, &
coefficient, size_max) bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
double precision, intent(out) :: coefficient(*)
integer (c_int64_t) , intent(in) , value :: size_max
end function qmckl_get_mo_basis_coefficient
end interface
#+end_src
** Initialization functions
To set the basis set, all the following functions need to be
@ -355,6 +386,34 @@ qmckl_exit_code qmckl_finalize_mo_basis(qmckl_context context) {
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
assert (ctx != NULL);
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
mem_info.size = ctx->ao_basis.ao_num * ctx->mo_basis.mo_num * sizeof(double);
double* new_array = (double*) qmckl_malloc(context, mem_info);
if (new_array == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_finalize_mo_basis",
NULL);
}
assert (ctx->mo_basis.coefficient != NULL);
if (ctx->mo_basis.coefficient_t != NULL) {
qmckl_exit_code rc = qmckl_free(context, ctx->mo_basis.coefficient);
if (rc != QMCKL_SUCCESS) {
return qmckl_failwith( context, rc,
"qmckl_finalize_mo_basis",
NULL);
}
}
for (int64_t i=0 ; i<ctx->ao_basis.ao_num ; ++i) {
for (int64_t j=0 ; j<ctx->mo_basis.mo_num ; ++j) {
new_array[i*ctx->mo_basis.mo_num + j] = ctx->mo_basis.coefficient[j*ctx->ao_basis.ao_num + i];
}
}
ctx->mo_basis.coefficient_t = new_array;
qmckl_exit_code rc = QMCKL_SUCCESS;
return rc;
}
@ -367,11 +426,18 @@ qmckl_exit_code qmckl_finalize_mo_basis(qmckl_context context) {
*** Get
#+begin_src c :comments org :tangle (eval h_func) :noweb yes
qmckl_exit_code qmckl_get_mo_basis_vgl(qmckl_context context, double* const mo_vgl);
qmckl_exit_code
qmckl_get_mo_basis_mo_vgl(qmckl_context context,
double* const mo_vgl,
const int64_t size_max);
#+end_src
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
qmckl_exit_code qmckl_get_mo_basis_vgl(qmckl_context context, double* const mo_vgl) {
qmckl_exit_code
qmckl_get_mo_basis_mo_vgl(qmckl_context context,
double* const mo_vgl,
const int64_t size_max)
{
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
return QMCKL_NULL_CONTEXT;
@ -388,7 +454,13 @@ qmckl_exit_code qmckl_get_mo_basis_vgl(qmckl_context context, double* const mo_v
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
assert (ctx != NULL);
size_t sze = 5 * ctx->point.num * ctx->mo_basis.mo_num;
const int64_t sze = ctx->point.num * 5 * ctx->mo_basis.mo_num;
if (size_max < sze) {
return qmckl_failwith( context,
QMCKL_INVALID_ARG_3,
"qmckl_get_mo_basis_mo_vgl",
"input array too small");
}
memcpy(mo_vgl, ctx->mo_basis.mo_vgl, sze * sizeof(double));
return QMCKL_SUCCESS;
@ -396,17 +468,84 @@ qmckl_exit_code qmckl_get_mo_basis_vgl(qmckl_context context, double* const mo_v
#+end_src
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
interface
integer(c_int32_t) function qmckl_get_mo_basis_vgl (context, mo_vgl) &
bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
interface
integer(c_int32_t) function qmckl_get_mo_basis_mo_vgl (context, &
mo_vgl, size_max) bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
double precision, intent(out) :: mo_vgl(*)
end function
end interface
integer (c_int64_t) , intent(in) , value :: context
double precision, intent(out) :: mo_vgl(*)
integer (c_int64_t) , intent(in) , value :: size_max
end function qmckl_get_mo_basis_mo_vgl
end interface
#+end_src
Uses the given array to compute the VGL.
#+begin_src c :comments org :tangle (eval h_func) :noweb yes
qmckl_exit_code
qmckl_get_mo_basis_mo_vgl_inplace (qmckl_context context,
double* const mo_vgl,
const int64_t size_max);
#+end_src
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
qmckl_exit_code
qmckl_get_mo_basis_mo_vgl_inplace (qmckl_context context,
double* const mo_vgl,
const int64_t size_max)
{
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
return qmckl_failwith( context,
QMCKL_INVALID_CONTEXT,
"qmckl_get_mo_basis_mo_vgl",
NULL);
}
qmckl_exit_code rc;
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
assert (ctx != NULL);
const int64_t sze = ctx->mo_basis.mo_num * 5 * ctx->point.num;
if (size_max < sze) {
return qmckl_failwith( context,
QMCKL_INVALID_ARG_3,
"qmckl_get_mo_basis_mo_vgl",
"input array too small");
}
rc = qmckl_context_touch(context);
if (rc != QMCKL_SUCCESS) return rc;
double* old_array = ctx->mo_basis.mo_vgl;
ctx->mo_basis.mo_vgl = mo_vgl;
rc = qmckl_provide_mo_vgl(context);
if (rc != QMCKL_SUCCESS) return rc;
ctx->mo_basis.mo_vgl = old_array;
return QMCKL_SUCCESS;
}
#+end_src
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
interface
integer(c_int32_t) function qmckl_get_mo_basis_mo_vgl_inplace (context, &
mo_vgl, size_max) bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
double precision, intent(out) :: mo_vgl(*)
integer (c_int64_t) , intent(in) , value :: size_max
end function qmckl_get_mo_basis_mo_vgl_inplace
end interface
#+end_src
*** Provide
@ -462,19 +601,19 @@ qmckl_exit_code qmckl_provide_mo_vgl(qmckl_context context)
if (mo_vgl == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_mo_basis_vgl",
"qmckl_mo_basis_mo_vgl",
NULL);
}
ctx->mo_basis.mo_vgl = mo_vgl;
}
rc = qmckl_compute_mo_basis_vgl(context,
ctx->ao_basis.ao_num,
ctx->mo_basis.mo_num,
ctx->point.num,
ctx->mo_basis.coefficient,
ctx->ao_basis.ao_vgl,
ctx->mo_basis.mo_vgl);
rc = qmckl_compute_mo_basis_mo_vgl(context,
ctx->ao_basis.ao_num,
ctx->mo_basis.mo_num,
ctx->point.num,
ctx->mo_basis.coefficient_t,
ctx->ao_basis.ao_vgl,
ctx->mo_basis.mo_vgl);
if (rc != QMCKL_SUCCESS) {
return rc;
}
@ -488,25 +627,33 @@ qmckl_exit_code qmckl_provide_mo_vgl(qmckl_context context)
*** Compute
:PROPERTIES:
:Name: qmckl_compute_mo_basis_vgl
:Name: qmckl_compute_mo_basis_mo_vgl
:CRetType: qmckl_exit_code
:FRetType: qmckl_exit_code
:END:
#+NAME: qmckl_mo_basis_vgl_args
| ~qmckl_context~ | ~context~ | in | Global state |
| ~int64_t~ | ~ao_num~ | in | Number of AOs |
| ~int64_t~ | ~mo_num~ | in | Number of MOs |
| ~int64_t~ | ~point_num~ | in | Number of points |
| ~double~ | ~coef_normalized[mo_num][ao_num]~ | in | AO to MO transformation matrix |
| ~double~ | ~ao_vgl[point_num][5][ao_num]~ | in | Value, gradients and Laplacian of the AOs |
| ~double~ | ~mo_vgl[point_num][5][mo_num]~ | out | Value, gradients and Laplacian of the MOs |
#+NAME: qmckl_mo_basis_mo_vgl_args
| Variable | Type | In/Out | Description |
|---------------------+--------------------------------+--------+-------------------------------------------------|
| ~context~ | ~qmckl_context~ | in | Global state |
| ~ao_num~ | ~int64_t~ | in | Number of AOs |
| ~mo_num~ | ~int64_t~ | in | Number of MOs |
| ~point_num~ | ~int64_t~ | in | Number of points |
| ~coef_normalized_t~ | ~double[mo_num][ao_num]~ | in | Transpose of the AO to MO transformation matrix |
| ~ao_vgl~ | ~double[point_num][5][ao_num]~ | in | Value, gradients and Laplacian of the AOs |
| ~mo_vgl~ | ~double[point_num][5][mo_num]~ | out | Value, gradients and Laplacian of the MOs |
The matrix of AO values is very sparse, so we use a sparse-dense
matrix multiplication instead of a dgemm, as exposed in
https://dx.doi.org/10.1007/978-3-642-38718-0_14.
#+begin_src f90 :comments org :tangle (eval f) :noweb yes
integer function qmckl_compute_mo_basis_vgl_f(context, &
integer function qmckl_compute_mo_basis_mo_vgl_doc_f(context, &
ao_num, mo_num, point_num, &
coef_normalized, ao_vgl, mo_vgl) &
coef_normalized_t, ao_vgl, mo_vgl) &
result(info)
use qmckl
implicit none
@ -514,55 +661,69 @@ integer function qmckl_compute_mo_basis_vgl_f(context, &
integer*8 , intent(in) :: ao_num, mo_num
integer*8 , intent(in) :: point_num
double precision , intent(in) :: ao_vgl(ao_num,5,point_num)
double precision , intent(in) :: coef_normalized(ao_num,mo_num)
double precision , intent(in) :: coef_normalized_t(mo_num,ao_num)
double precision , intent(out) :: mo_vgl(mo_num,5,point_num)
character :: TransA, TransB
double precision :: alpha, beta
integer*8 :: M, N, K, LDA, LDB, LDC, i,j
integer*8 :: i,j,k
double precision :: c1, c2, c3, c4, c5
TransA = 'T'
TransB = 'N'
M = mo_num
N = point_num*5_8
K = int(ao_num,8)
alpha = 1.d0
beta = 0.d0
LDA = size(coef_normalized,1)
LDB = size(ao_vgl,1)
LDC = size(mo_vgl,1)
do j=1,point_num
mo_vgl(:,:,j) = 0.d0
do k=1,ao_num
if (ao_vgl(k,1,j) /= 0.d0) then
c1 = ao_vgl(k,1,j)
c2 = ao_vgl(k,2,j)
c3 = ao_vgl(k,3,j)
c4 = ao_vgl(k,4,j)
c5 = ao_vgl(k,5,j)
do i=1,mo_num
mo_vgl(i,1,j) = mo_vgl(i,1,j) + coef_normalized_t(i,k) * c1
mo_vgl(i,2,j) = mo_vgl(i,2,j) + coef_normalized_t(i,k) * c2
mo_vgl(i,3,j) = mo_vgl(i,3,j) + coef_normalized_t(i,k) * c3
mo_vgl(i,4,j) = mo_vgl(i,4,j) + coef_normalized_t(i,k) * c4
mo_vgl(i,5,j) = mo_vgl(i,5,j) + coef_normalized_t(i,k) * c5
end do
end if
end do
end do
info = qmckl_dgemm(context,TransA, TransB, M, N, K, alpha, &
coef_normalized, int(size(coef_normalized,1),8), &
ao_vgl, int(size(ao_vgl,1),8), beta, &
mo_vgl,LDC)
info = QMCKL_SUCCESS
end function qmckl_compute_mo_basis_vgl_f
end function qmckl_compute_mo_basis_mo_vgl_doc_f
#+end_src
#+CALL: generate_c_header(table=qmckl_mo_basis_vgl_args,rettyp=get_value("CRetType"),fname="qmckl_compute_mo_basis_vgl"))
#+CALL: generate_c_header(table=qmckl_mo_basis_mo_vgl_args,rettyp=get_value("CRetType"),fname="qmckl_compute_mo_basis_mo_vgl"))
#+RESULTS:
#+begin_src c :tangle (eval h_func) :comments org
qmckl_exit_code qmckl_compute_mo_basis_vgl (
const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* coef_normalized,
const double* ao_vgl,
double* const mo_vgl );
qmckl_exit_code qmckl_compute_mo_basis_mo_vgl (
const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* coef_normalized_t,
const double* ao_vgl,
double* const mo_vgl );
#+end_src
#+CALL: generate_c_header(table=qmckl_mo_basis_mo_vgl_args,rettyp=get_value("CRetType"),fname="qmckl_compute_mo_basis_mo_vgl_doc"))
#+CALL: generate_c_interface(table=qmckl_mo_basis_vgl_args,rettyp=get_value("CRetType"),fname="qmckl_compute_mo_basis_vgl"))
#+RESULTS:
#+begin_src c :tangle (eval h_func) :comments org
qmckl_exit_code qmckl_compute_mo_basis_mo_vgl_doc (
const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* coef_normalized_t,
const double* ao_vgl,
double* const mo_vgl );
#+end_src
#+CALL: generate_c_interface(table=qmckl_mo_basis_mo_vgl_args,rettyp=get_value("CRetType"),fname="qmckl_compute_mo_basis_mo_vgl_doc"))
#+RESULTS:
#+begin_src f90 :tangle (eval f) :comments org :exports none
integer(c_int32_t) function qmckl_compute_mo_basis_vgl &
(context, ao_num, mo_num, point_num, coef_normalized, ao_vgl, mo_vgl) &
bind(C) result(info)
integer(c_int32_t) function qmckl_compute_mo_basis_mo_vgl_doc &
(context, ao_num, mo_num, point_num, coef_normalized_t, ao_vgl, mo_vgl) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
@ -571,15 +732,176 @@ end function qmckl_compute_mo_basis_vgl_f
integer (c_int64_t) , intent(in) , value :: ao_num
integer (c_int64_t) , intent(in) , value :: mo_num
integer (c_int64_t) , intent(in) , value :: point_num
real (c_double ) , intent(in) :: coef_normalized(ao_num,mo_num)
real (c_double ) , intent(in) :: coef_normalized_t(ao_num,mo_num)
real (c_double ) , intent(in) :: ao_vgl(ao_num,5,point_num)
real (c_double ) , intent(out) :: mo_vgl(mo_num,5,point_num)
integer(c_int32_t), external :: qmckl_compute_mo_basis_vgl_f
info = qmckl_compute_mo_basis_vgl_f &
(context, ao_num, mo_num, point_num, coef_normalized, ao_vgl, mo_vgl)
integer(c_int32_t), external :: qmckl_compute_mo_basis_mo_vgl_doc_f
info = qmckl_compute_mo_basis_mo_vgl_doc_f &
(context, ao_num, mo_num, point_num, coef_normalized_t, ao_vgl, mo_vgl)
end function qmckl_compute_mo_basis_vgl
end function qmckl_compute_mo_basis_mo_vgl_doc
#+end_src
#+begin_src c :tangle (eval c) :comments org
qmckl_exit_code
qmckl_compute_mo_basis_mo_vgl (const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* coef_normalized_t,
const double* ao_vgl,
double* const mo_vgl )
{
#ifdef HAVE_HPC
return qmckl_compute_mo_basis_mo_vgl_hpc (context, ao_num, mo_num, point_num, coef_normalized_t, ao_vgl, mo_vgl);
#else
return qmckl_compute_mo_basis_mo_vgl_doc (context, ao_num, mo_num, point_num, coef_normalized_t, ao_vgl, mo_vgl);
#endif
}
#+end_src
*** HPC version
#+begin_src c :tangle (eval h_func) :comments org
#ifdef HAVE_HPC
qmckl_exit_code
qmckl_compute_mo_basis_mo_vgl_hpc (const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* coef_normalized_t,
const double* ao_vgl,
double* const mo_vgl );
#endif
#+end_src
#+begin_src c :tangle (eval c) :comments org
#ifdef HAVE_HPC
qmckl_exit_code
qmckl_compute_mo_basis_mo_vgl_hpc (const qmckl_context context,
const int64_t ao_num,
const int64_t mo_num,
const int64_t point_num,
const double* restrict coef_normalized_t,
const double* restrict ao_vgl,
double* restrict const mo_vgl )
{
#ifdef HAVE_OPENMP
#pragma omp parallel for
#endif
for (int64_t ipoint=0 ; ipoint < point_num ; ++ipoint) {
double* restrict const vgl1 = &(mo_vgl[ipoint*5*mo_num]);
const double* restrict avgl1 = &(ao_vgl[ipoint*5*ao_num]);
double* restrict const vgl2 = vgl1 + mo_num;
double* restrict const vgl3 = vgl1 + (mo_num << 1);
double* restrict const vgl4 = vgl1 + (mo_num << 1) + mo_num;
double* restrict const vgl5 = vgl1 + (mo_num << 2);
const double* restrict avgl2 = avgl1 + ao_num;
const double* restrict avgl3 = avgl1 + (ao_num << 1);
const double* restrict avgl4 = avgl1 + (ao_num << 1) + ao_num;
const double* restrict avgl5 = avgl1 + (ao_num << 2);
for (int64_t i=0 ; i<mo_num ; ++i) {
vgl1[i] = 0.;
vgl2[i] = 0.;
vgl3[i] = 0.;
vgl4[i] = 0.;
vgl5[i] = 0.;
}
int64_t nidx=0;
int64_t idx[ao_num];
double av1[ao_num];
double av2[ao_num];
double av3[ao_num];
double av4[ao_num];
double av5[ao_num];
for (int64_t k=0 ; k<ao_num ; ++k) {
const double* restrict ck1 = coef_normalized_t + k*mo_num;
if (avgl1[k] != 0.) {
idx[nidx] = k;
av1[nidx] = avgl1[k];
av2[nidx] = avgl2[k];
av3[nidx] = avgl3[k];
av4[nidx] = avgl4[k];
av5[nidx] = avgl5[k];
++nidx;
}
}
int64_t n;
for (n=0 ; n < nidx-4 ; n+=4) {
int64_t k = idx[n];
const double* restrict ck1 = coef_normalized_t + idx[n ]*mo_num;
const double* restrict ck2 = coef_normalized_t + idx[n+1]*mo_num;
const double* restrict ck3 = coef_normalized_t + idx[n+2]*mo_num;
const double* restrict ck4 = coef_normalized_t + idx[n+3]*mo_num;
const double a11 = av1[n ];
const double a21 = av1[n+1];
const double a31 = av1[n+2];
const double a41 = av1[n+3];
const double a12 = av2[n ];
const double a22 = av2[n+1];
const double a32 = av2[n+2];
const double a42 = av2[n+3];
const double a13 = av3[n ];
const double a23 = av3[n+1];
const double a33 = av3[n+2];
const double a43 = av3[n+3];
const double a14 = av4[n ];
const double a24 = av4[n+1];
const double a34 = av4[n+2];
const double a44 = av4[n+3];
const double a15 = av5[n ];
const double a25 = av5[n+1];
const double a35 = av5[n+2];
const double a45 = av5[n+3];
#ifdef HAVE_OPENMP
#pragma omp simd
#endif
for (int64_t i=0 ; i<mo_num ; ++i) {
vgl1[i] = vgl1[i] + ck1[i] * a11 + ck2[i] * a21 + ck3[i] * a31 + ck4[i] * a41;
vgl2[i] = vgl2[i] + ck1[i] * a12 + ck2[i] * a22 + ck3[i] * a32 + ck4[i] * a42;
vgl3[i] = vgl3[i] + ck1[i] * a13 + ck2[i] * a23 + ck3[i] * a33 + ck4[i] * a43;
vgl4[i] = vgl4[i] + ck1[i] * a14 + ck2[i] * a24 + ck3[i] * a34 + ck4[i] * a44;
vgl5[i] = vgl5[i] + ck1[i] * a15 + ck2[i] * a25 + ck3[i] * a35 + ck4[i] * a45;
}
}
int64_t n0 = nidx-4;
n0 = n0 < 0 ? 0 : n0;
for (int64_t n=n0 ; n < nidx ; n+=1) {
const double* restrict ck = coef_normalized_t + idx[n]*mo_num;
const double a1 = av1[n];
const double a2 = av2[n];
const double a3 = av3[n];
const double a4 = av4[n];
const double a5 = av5[n];
#ifdef HAVE_OPENMP
#pragma omp simd
#endif
for (int64_t i=0 ; i<mo_num ; ++i) {
vgl1[i] += ck[i] * a1;
vgl2[i] += ck[i] * a2;
vgl3[i] += ck[i] * a3;
vgl4[i] += ck[i] * a4;
vgl5[i] += ck[i] * a5;
}
}
}
return QMCKL_SUCCESS;
}
#endif
#+end_src
*** Test
@ -772,7 +1094,7 @@ assert (rc == QMCKL_SUCCESS);
assert(qmckl_mo_basis_provided(context));
double mo_vgl[walk_num*elec_num][5][chbrclf_mo_num];
rc = qmckl_get_mo_basis_vgl(context, &(mo_vgl[0][0][0]));
rc = qmckl_get_mo_basis_mo_vgl(context, &(mo_vgl[0][0][0]), walk_num*elec_num*5*chbrclf_mo_num);
assert (rc == QMCKL_SUCCESS);
// Test overlap of MO
@ -807,7 +1129,7 @@ assert (rc == QMCKL_SUCCESS);
//
// // Calculate value of MO (1st electron)
// double mo_vgl[5][walk_num][elec_num][chbrclf_mo_num];
// rc = qmckl_get_mo_basis_vgl(context, &(mo_vgl[0][0][0][0]));
// rc = qmckl_get_mo_basis_mo_vgl(context, &(mo_vgl[0][0][0][0]));
// assert (rc == QMCKL_SUCCESS);
// ovlmo1 += mo_vgl[0][0][0][0]*mo_vgl[0][0][0][0]*dr3;
// }

6
org/qmckl_numprec.org
View File

@ -250,19 +250,19 @@ qmckl_exit_code qmckl_set_numprec_range(const qmckl_context context, const int r
# Fortran interface
#+begin_src f90 :tangle (eval fh_func)
interface
integer (qmckl_exit_code) function qmckl_numprec_set_range(context, range) bind(C)
integer (qmckl_exit_code) function qmckl_set_numprec_range(context, range) bind(C)
use, intrinsic :: iso_c_binding
import
integer (qmckl_context), intent(in), value :: context
integer (c_int32_t), intent(in), value :: range
end function qmckl_numprec_set_range
end function qmckl_set_numprec_range
end interface
#+end_src
~qmckl_get_numprec_range~ returns the value of the numerical range in the context.
#+begin_src c :comments org :tangle (eval h_func) :exports none
int32_t qmckl_get_numprec_get_range(const qmckl_context context);
int32_t qmckl_get_numprec_range(const qmckl_context context);
#+end_src
# Source

7
org/qmckl_point.org
View File

@ -257,7 +257,8 @@ end interface
enough, we overwrite the data contained in them.
To set the data relative to the points in the context, one of the
following functions need to be called.
following functions need to be called. Here, ~num~ is the number of
points to set.
#+begin_src c :comments org :tangle (eval h_func)
qmckl_exit_code qmckl_set_point (qmckl_context context,
@ -348,7 +349,7 @@ qmckl_set_point (qmckl_context context,
#+begin_src f90 :comments org :tangle (eval fh_func) :noweb yes
interface
integer(c_int32_t) function qmckl_set_point(context, &
transp, coord, size_max) bind(C)
transp, coord, num) bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
@ -356,7 +357,7 @@ interface
integer (c_int64_t) , intent(in) , value :: context
character(c_char) , intent(in) , value :: transp
real (c_double ) , intent(in) :: coord(*)
integer (c_int64_t) , intent(in) , value :: size_max
integer (c_int64_t) , intent(in) , value :: num
end function
end interface
#+end_src

4
tools/theme.setup
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@ -6,7 +6,9 @@
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="qmckl.css" type="text/css" />
#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate latexpreview
# STARTUP: align fold nodlcheck hidestars oddeven lognotestate latexpreview
#+STARTUP: showeverything
#+AUTHOR: TREX CoE
#+LANGUAGE: en