mirror of
https://github.com/TREX-CoE/qmckl.git
synced 2024-07-01 08:56:29 +02:00
1178 lines
35 KiB
Org Mode
1178 lines
35 KiB
Org Mode
#+TITLE: Nucleus
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#+SETUPFILE: ../tools/theme.setup
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#+INCLUDE: ../tools/lib.org
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All the data relative to the molecular geometry is described here.
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* Headers :noexport:
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#+begin_src elisp :noexport :results none
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( org-babel-lob-ingest "../tools/lib.org")
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#+end_src
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#+begin_src c :tangle (eval h_private_type)
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#ifndef QMCKL_NUCLEUS_HPT
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#define QMCKL_NUCLEUS_HPT
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#include <stdbool.h>
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#+end_src
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#+begin_src c :tangle (eval c_test) :noweb yes
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#include "qmckl.h"
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#include <assert.h>
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#include <stdio.h>
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#include <math.h>
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include "chbrclf.h"
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int main() {
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qmckl_context context;
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context = qmckl_context_create();
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#+end_src
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#+begin_src c :tangle (eval c)
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#ifdef HAVE_STDINT_H
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#include <stdint.h>
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#elif HAVE_INTTYPES_H
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#include <inttypes.h>
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#endif
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#include <stdlib.h>
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#include <string.h>
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#include <stdbool.h>
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#include <assert.h>
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#include <math.h>
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#include <stdio.h>
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#include "qmckl.h"
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#include "qmckl_context_private_type.h"
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#include "qmckl_memory_private_type.h"
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#include "qmckl_memory_private_func.h"
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#include "qmckl_nucleus_private_func.h"
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#+end_src
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* Context
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The following data stored in the context:
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| ~uninitialized~ | int32_t | Keeps bit set for uninitialized data |
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| ~num~ | int64_t | Total number of nuclei |
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| ~provided~ | bool | If true, ~nucleus~ is valid |
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| ~charge~ | double[num] | Nuclear charges |
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| ~coord~ | double[3][num] | Nuclear coordinates, in transposed format |
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| ~nn_distance~ | double[num][num] | Nucleus-nucleus distances |
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| ~nn_distance_date~ | int64_t | Date when Nucleus-nucleus distances were computed |
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| ~nn_distance_rescaled~ | double[num][num] | Nucleus-nucleus rescaled distances |
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| ~nn_distance_rescaled_date~ | int64_t | Date when Nucleus-nucleus rescaled distances were computed |
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| ~repulsion~ | double | Nuclear repulsion energy |
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| ~repulsion_date~ | int64_t | Date when the nuclear repulsion energy was computed |
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| ~rescale_factor_kappa~ | double | The distance scaling factor |
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** Data structure
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#+begin_src c :comments org :tangle (eval h_private_type)
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typedef struct qmckl_nucleus_struct {
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int64_t num;
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int64_t repulsion_date;
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int64_t nn_distance_date;
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int64_t nn_distance_rescaled_date;
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double* coord;
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double* charge;
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double* nn_distance;
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double* nn_distance_rescaled;
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double repulsion;
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double rescale_factor_kappa;
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int32_t uninitialized;
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bool provided;
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} qmckl_nucleus_struct;
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#+end_src
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The ~uninitialized~ integer contains one bit set to one for each
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initialization function which has not been called. It becomes equal
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to zero after all initialization functions have been called. The
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struct is then initialized and ~provided == true~.
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Some values are initialized by default, and are not concerned by
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this mechanism.
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#+begin_src c :comments org :tangle (eval h_private_func)
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qmckl_exit_code qmckl_init_nucleus(qmckl_context context);
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#+end_src
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#+begin_src c :comments org :tangle (eval c)
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qmckl_exit_code qmckl_init_nucleus(qmckl_context context) {
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return false;
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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ctx->nucleus.uninitialized = (1 << 3) - 1;
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/* Default values */
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ctx->nucleus.rescale_factor_kappa = 1.0;
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return QMCKL_SUCCESS;
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}
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#+end_src
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** Access functions
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#+begin_src c :comments org :tangle (eval h_func) :exports none
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qmckl_exit_code qmckl_get_nucleus_num (const qmckl_context context, int64_t* const num);
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qmckl_exit_code qmckl_get_nucleus_charge (const qmckl_context context, double* const charge);
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qmckl_exit_code qmckl_get_nucleus_coord (const qmckl_context context, const char transp, double* const coord);
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qmckl_exit_code qmckl_get_nucleus_rescale_factor (const qmckl_context context, double* const rescale_factor_kappa);
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#+end_src
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#+NAME:post
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#+begin_src c :exports none
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if ( (ctx->nucleus.uninitialized & mask) != 0) {
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return NULL;
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}
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#+end_src
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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qmckl_exit_code
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qmckl_get_nucleus_num (const qmckl_context context, int64_t* const num) {
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return QMCKL_INVALID_CONTEXT;
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}
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if (num == NULL) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_get_nucleus_num",
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"num is a null pointer");
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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int32_t mask = 1 << 0;
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if ( (ctx->nucleus.uninitialized & mask) != 0) {
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,*num = (int64_t) 0;
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return qmckl_failwith( context,
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QMCKL_NOT_PROVIDED,
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"qmckl_get_nucleus_num",
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"nucleus data is not provided");
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}
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assert (ctx->nucleus.num >= (int64_t) 0);
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,*num = ctx->nucleus.num;
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return QMCKL_SUCCESS;
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}
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qmckl_exit_code
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qmckl_get_nucleus_charge (const qmckl_context context, double* const charge) {
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return QMCKL_INVALID_CONTEXT;
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}
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if (charge == NULL) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_get_nucleus_charge",
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"charge is a null pointer");
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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int32_t mask = 1 << 1;
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if ( (ctx->nucleus.uninitialized & mask) != 0) {
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return qmckl_failwith( context,
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QMCKL_NOT_PROVIDED,
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"qmckl_get_nucleus_charge",
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"nucleus data is not provided");
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}
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assert (ctx->nucleus.charge != NULL);
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int64_t nucl_num = ctx->nucleus.num;
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memcpy(charge, ctx->nucleus.charge, nucl_num*sizeof(double));
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return QMCKL_SUCCESS;
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}
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qmckl_exit_code
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qmckl_get_nucleus_rescale_factor (const qmckl_context context,
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double* const rescale_factor_kappa)
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{
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return QMCKL_INVALID_CONTEXT;
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}
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if (rescale_factor_kappa == NULL) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_get_nucleus_rescale_factor",
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"rescale_factor_kappa is a null pointer");
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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assert (ctx->nucleus.rescale_factor_kappa > 0.0);
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(*rescale_factor_kappa) = ctx->nucleus.rescale_factor_kappa;
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return QMCKL_SUCCESS;
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}
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qmckl_exit_code
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qmckl_get_nucleus_coord (const qmckl_context context, const char transp, double* const coord) {
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return QMCKL_INVALID_CONTEXT;
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}
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if (transp != 'N' && transp != 'T') {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_get_nucleus_coord",
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"transp should be 'N' or 'T'");
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}
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if (coord == NULL) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_3,
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"qmckl_get_nucleus_coord",
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"coord is a null pointer");
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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int32_t mask = 1 << 2;
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if ( (ctx->nucleus.uninitialized & mask) != 0) {
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return qmckl_failwith( context,
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QMCKL_NOT_PROVIDED,
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"qmckl_get_nucleus_coord",
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"nucleus data is not provided");
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}
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int64_t nucl_num = ctx->nucleus.num;
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assert (ctx->nucleus.coord != NULL);
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if (transp == 'N') {
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qmckl_exit_code rc;
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rc = qmckl_transpose(context, nucl_num, 3,
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ctx->nucleus.coord, nucl_num,
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coord, 3);
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if (rc != QMCKL_SUCCESS) return rc;
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} else {
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memcpy(coord, ctx->nucleus.coord, 3*nucl_num*sizeof(double));
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}
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return QMCKL_SUCCESS;
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}
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#+end_src
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When all the data relative to nuclei have been set, the following
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function returns ~true~.
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#+begin_src c :comments org :tangle (eval h_func)
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bool qmckl_nucleus_provided (const qmckl_context context);
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#+end_src
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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bool qmckl_nucleus_provided(const qmckl_context context) {
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return false;
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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assert (ctx != NULL);
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return ctx->nucleus.provided;
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}
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#+end_src
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** Initialization functions
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To set the data relative to the nuclei in the context, the
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following functions need to be called.
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#+begin_src c :comments org :tangle (eval h_func)
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qmckl_exit_code qmckl_set_nucleus_num (qmckl_context context, const int64_t num);
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qmckl_exit_code qmckl_set_nucleus_charge (qmckl_context context, const double* charge);
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qmckl_exit_code qmckl_set_nucleus_coord (qmckl_context context, const char transp, const double* coord);
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qmckl_exit_code qmckl_set_nucleus_rescale_factor (qmckl_context context, const double rescale_factor_kappa);
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#+end_src
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#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
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interface
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integer(c_int32_t) function qmckl_set_nucleus_num(context, num) &
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bind(C)
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use, intrinsic :: iso_c_binding
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import
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implicit none
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integer (c_int64_t) , intent(in) , value :: context
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integer (c_int64_t) , intent(in) , value :: num
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end function
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end interface
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interface
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integer(c_int32_t) function qmckl_set_nucleus_charge(context, charge) &
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bind(C)
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use, intrinsic :: iso_c_binding
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import
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implicit none
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integer (c_int64_t) , intent(in) , value :: context
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real (c_double) , intent(in) :: charge(*)
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end function
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end interface
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interface
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integer(c_int32_t) function qmckl_set_nucleus_coord(context, transp, coord) &
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bind(C)
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use, intrinsic :: iso_c_binding
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import
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implicit none
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integer (c_int64_t) , intent(in) , value :: context
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character(c_char) , intent(in) , value :: transp
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real (c_double) , intent(in) :: coord(*)
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end function
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end interface
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#+end_src
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#+NAME:pre2
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#+begin_src c :exports none
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if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
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return QMCKL_NULL_CONTEXT;
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}
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qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
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#+end_src
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#+NAME:post2
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#+begin_src c :exports none
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ctx->nucleus.uninitialized &= ~mask;
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ctx->nucleus.provided = (ctx->nucleus.uninitialized == 0);
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return QMCKL_SUCCESS;
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#+end_src
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To set the number of nuclei, use
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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qmckl_exit_code
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qmckl_set_nucleus_num(qmckl_context context, const int64_t num) {
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<<pre2>>
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if (num <= 0) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_set_nucleus_num",
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"num <= 0");
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}
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int32_t mask = 1 << 0;
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ctx->nucleus.num = num;
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<<post2>>
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}
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#+end_src
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The following function sets the nuclear charges of all the atoms.
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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qmckl_exit_code
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qmckl_set_nucleus_charge(qmckl_context context, const double* charge) {
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<<pre2>>
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if (charge == NULL) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_set_nucleus_charge",
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"charge is a null pointer");
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}
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int64_t num;
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qmckl_exit_code rc;
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int32_t mask = 1 << 1;
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rc = qmckl_get_nucleus_num(context, &num);
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if (rc != QMCKL_SUCCESS) return rc;
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if (ctx->nucleus.charge != NULL) {
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qmckl_free(context, ctx->nucleus.charge);
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ctx->nucleus.charge= NULL;
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}
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qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
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mem_info.size = num*sizeof(double);
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assert (ctx->nucleus.charge == NULL);
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ctx->nucleus.charge = (double*) qmckl_malloc(context, mem_info);
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if (ctx->nucleus.charge == NULL) {
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return qmckl_failwith( context,
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QMCKL_ALLOCATION_FAILED,
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"qmckl_set_nucleus_charge",
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NULL);
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}
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ctx->nucleus.charge= memcpy(ctx->nucleus.charge, charge, num*sizeof(double));
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assert (ctx->nucleus.charge != NULL);
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<<post2>>
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}
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#+end_src
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The following function sets the rescale parameter for the nuclear distances.
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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qmckl_exit_code
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qmckl_set_nucleus_rescale_factor(qmckl_context context, const double rescale_factor_kappa) {
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<<pre2>>
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if (rescale_factor_kappa <= 0.0) {
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return qmckl_failwith( context,
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QMCKL_INVALID_ARG_2,
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"qmckl_set_nucleus_rescale_factor",
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"rescale_factor_kappa cannot be <= 0.");
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}
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ctx->nucleus.rescale_factor_kappa = rescale_factor_kappa;
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return QMCKL_SUCCESS;
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}
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#+end_src
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The following function sets the nuclear coordinates of all the
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atoms. The coordinates should be given in atomic units.
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
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qmckl_exit_code
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qmckl_set_nucleus_coord(qmckl_context context, const char transp, const double* coord) {
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<<pre2>>
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int64_t nucl_num = (int64_t) 0;
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qmckl_exit_code rc;
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int32_t mask = 1 << 2;
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rc = qmckl_get_nucleus_num(context, &nucl_num);
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if (rc != QMCKL_SUCCESS) return rc;
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if (ctx->nucleus.coord != NULL) {
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qmckl_free(context, ctx->nucleus.coord);
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ctx->nucleus.coord = NULL;
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}
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qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
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mem_info.size = 3*nucl_num*sizeof(double);
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assert(ctx->nucleus.coord == NULL);
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ctx->nucleus.coord = (double*) qmckl_malloc(context, mem_info);
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if (coord == NULL) {
|
|
return qmckl_failwith( context,
|
|
QMCKL_ALLOCATION_FAILED,
|
|
"qmckl_set_nucleus_coord",
|
|
NULL);
|
|
}
|
|
if (transp == 'N') {
|
|
rc = qmckl_transpose(context, 3, nucl_num,
|
|
coord, 3,
|
|
ctx->nucleus.coord, nucl_num);
|
|
if (rc != QMCKL_SUCCESS) return rc;
|
|
} else {
|
|
memcpy(ctx->nucleus.coord, coord, 3*nucl_num*sizeof(double));
|
|
}
|
|
|
|
<<post2>>
|
|
}
|
|
#+end_src
|
|
|
|
** Test
|
|
|
|
#+begin_src c :tangle (eval c_test)
|
|
const int64_t nucl_num = chbrclf_nucl_num;
|
|
const double* nucl_charge = chbrclf_charge;
|
|
const double* nucl_coord = &(chbrclf_nucl_coord[0][0]);
|
|
const double nucl_rescale_factor_kappa = 2.0;
|
|
|
|
/* --- */
|
|
|
|
qmckl_exit_code rc;
|
|
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
int64_t n;
|
|
rc = qmckl_get_nucleus_num (context, &n);
|
|
assert(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
|
|
rc = qmckl_set_nucleus_num (context, nucl_num);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
rc = qmckl_get_nucleus_num (context, &n);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
assert(n == nucl_num);
|
|
|
|
double k;
|
|
rc = qmckl_get_nucleus_rescale_factor (context, &k);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
assert(k == 1.0);
|
|
|
|
|
|
rc = qmckl_set_nucleus_rescale_factor (context, nucl_rescale_factor_kappa);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
|
|
rc = qmckl_get_nucleus_rescale_factor (context, &k);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
assert(k == nucl_rescale_factor_kappa);
|
|
|
|
double nucl_coord2[3*nucl_num];
|
|
|
|
rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2);
|
|
assert(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
rc = qmckl_set_nucleus_coord (context, 'T', &(nucl_coord[0]));
|
|
assert(rc == QMCKL_SUCCESS);
|
|
|
|
assert(!qmckl_nucleus_provided(context));
|
|
|
|
rc = qmckl_get_nucleus_coord (context, 'N', nucl_coord2);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
for (size_t k=0 ; k<3 ; ++k) {
|
|
for (size_t i=0 ; i<nucl_num ; ++i) {
|
|
assert( nucl_coord[nucl_num*k+i] == nucl_coord2[3*i+k] );
|
|
}
|
|
}
|
|
|
|
rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
for (size_t i=0 ; i<3*nucl_num ; ++i) {
|
|
assert( nucl_coord[i] == nucl_coord2[i] );
|
|
}
|
|
|
|
double nucl_charge2[nucl_num];
|
|
|
|
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
|
|
assert(rc == QMCKL_NOT_PROVIDED);
|
|
|
|
rc = qmckl_set_nucleus_charge(context, nucl_charge);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
|
|
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
|
|
assert(rc == QMCKL_SUCCESS);
|
|
for (size_t i=0 ; i<nucl_num ; ++i) {
|
|
assert( nucl_charge[i] == nucl_charge2[i] );
|
|
}
|
|
assert(qmckl_nucleus_provided(context));
|
|
#+end_src
|
|
|
|
* Computation
|
|
|
|
The computed data is stored in the context so that it can be reused
|
|
by different kernels. To ensure that the data is valid, for each
|
|
computed data the date of the context is stored when it is computed.
|
|
To know if some data needs to be recomputed, we check if the date of
|
|
the dependencies are more recent than the date of the data to
|
|
compute. If it is the case, then the data is recomputed and the
|
|
current date is stored.
|
|
|
|
** Nucleus-nucleus distances
|
|
|
|
*** Get
|
|
|
|
#+begin_src c :comments org :tangle (eval h_func) :noweb yes
|
|
qmckl_exit_code qmckl_get_nucleus_nn_distance(qmckl_context context, double* distance);
|
|
#+end_src
|
|
|
|
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_get_nucleus_nn_distance(qmckl_context context, double* distance)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_exit_code rc = qmckl_provide_nn_distance(context);
|
|
if (rc != QMCKL_SUCCESS) return rc;
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
size_t sze = ctx->nucleus.num * ctx->nucleus.num;
|
|
memcpy(distance, ctx->nucleus.nn_distance, sze * sizeof(double));
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
|
|
interface
|
|
integer(c_int32_t) function qmckl_get_nucleus_nn_distance(context, distance) &
|
|
bind(C)
|
|
use, intrinsic :: iso_c_binding
|
|
import
|
|
implicit none
|
|
integer (c_int64_t) , intent(in) , value :: context
|
|
real (c_double ) , intent(out) :: distance(*)
|
|
end function
|
|
end interface
|
|
#+end_src
|
|
|
|
*** Provide :noexport:
|
|
|
|
#+begin_src c :comments org :tangle (eval h_private_func) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nn_distance(qmckl_context context);
|
|
#+end_src
|
|
|
|
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nn_distance(qmckl_context context)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
if (!ctx->nucleus.provided) return QMCKL_NOT_PROVIDED;
|
|
|
|
/* Allocate array */
|
|
if (ctx->nucleus.nn_distance == NULL) {
|
|
|
|
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
|
|
mem_info.size = ctx->nucleus.num * ctx->nucleus.num * sizeof(double);
|
|
double* nn_distance = (double*) qmckl_malloc(context, mem_info);
|
|
|
|
if (nn_distance == NULL) {
|
|
return qmckl_failwith( context,
|
|
QMCKL_ALLOCATION_FAILED,
|
|
"qmckl_nn_distance",
|
|
NULL);
|
|
}
|
|
ctx->nucleus.nn_distance = nn_distance;
|
|
}
|
|
|
|
qmckl_exit_code rc =
|
|
qmckl_compute_nn_distance(context,
|
|
ctx->nucleus.num,
|
|
ctx->nucleus.coord,
|
|
ctx->nucleus.nn_distance);
|
|
if (rc != QMCKL_SUCCESS) {
|
|
return rc;
|
|
}
|
|
|
|
ctx->nucleus.nn_distance_date = ctx->date;
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
*** Compute
|
|
|
|
#+NAME: qmckl_nn_distance_args
|
|
| qmckl_context | context | in | Global state |
|
|
| int64_t | nucl_num | in | Number of nuclei |
|
|
| double | coord[3][nucl_num] | in | Nuclear coordinates (au) |
|
|
| double | nn_distance[nucl_num][nucl_num] | out | Nucleus-nucleus distances (au) |
|
|
|
|
#+begin_src f90 :comments org :tangle (eval f) :noweb yes
|
|
integer function qmckl_compute_nn_distance_f(context, nucl_num, coord, nn_distance) &
|
|
result(info)
|
|
use qmckl
|
|
implicit none
|
|
integer(qmckl_context), intent(in) :: context
|
|
integer*8 , intent(in) :: nucl_num
|
|
double precision , intent(in) :: coord(nucl_num,3)
|
|
double precision , intent(out) :: nn_distance(nucl_num,nucl_num)
|
|
|
|
integer*8 :: k
|
|
|
|
info = QMCKL_SUCCESS
|
|
|
|
if (context == QMCKL_NULL_CONTEXT) then
|
|
info = QMCKL_INVALID_CONTEXT
|
|
return
|
|
endif
|
|
|
|
if (nucl_num <= 0) then
|
|
info = QMCKL_INVALID_ARG_2
|
|
return
|
|
endif
|
|
|
|
info = qmckl_distance(context, 'T', 'T', nucl_num, nucl_num, &
|
|
coord, nucl_num, &
|
|
coord, nucl_num, &
|
|
nn_distance, nucl_num)
|
|
|
|
end function qmckl_compute_nn_distance_f
|
|
#+end_src
|
|
|
|
#+begin_src c :tangle (eval h_private_func) :comments org :exports none
|
|
qmckl_exit_code qmckl_compute_nn_distance (
|
|
const qmckl_context context,
|
|
const int64_t nucl_num,
|
|
const double* coord,
|
|
double* const nn_distance );
|
|
#+end_src
|
|
|
|
|
|
#+CALL: generate_c_interface(table=qmckl_nn_distance_args,rettyp="qmckl_exit_code",fname="qmckl_compute_nn_distance")
|
|
|
|
#+RESULTS:
|
|
#+begin_src f90 :tangle (eval f) :comments org :exports none
|
|
integer(c_int32_t) function qmckl_compute_nn_distance &
|
|
(context, nucl_num, coord, nn_distance) &
|
|
bind(C) result(info)
|
|
|
|
use, intrinsic :: iso_c_binding
|
|
implicit none
|
|
|
|
integer (c_int64_t) , intent(in) , value :: context
|
|
integer (c_int64_t) , intent(in) , value :: nucl_num
|
|
real (c_double ) , intent(in) :: coord(nucl_num,3)
|
|
real (c_double ) , intent(out) :: nn_distance(nucl_num,nucl_num)
|
|
|
|
integer(c_int32_t), external :: qmckl_compute_nn_distance_f
|
|
info = qmckl_compute_nn_distance_f &
|
|
(context, nucl_num, coord, nn_distance)
|
|
|
|
end function qmckl_compute_nn_distance
|
|
#+end_src
|
|
|
|
*** Test
|
|
|
|
#+begin_src c :tangle (eval c_test)
|
|
/* Reference input data */
|
|
|
|
assert(qmckl_nucleus_provided(context));
|
|
|
|
double distance[nucl_num*nucl_num];
|
|
rc = qmckl_get_nucleus_nn_distance(context, distance);
|
|
assert(distance[0] == 0.);
|
|
assert(distance[1] == distance[nucl_num]);
|
|
assert(fabs(distance[1]-2.070304721365169) < 1.e-12);
|
|
|
|
#+end_src
|
|
|
|
|
|
** Nucleus-nucleus rescaled distances
|
|
|
|
*** Get
|
|
|
|
#+begin_src c :comments org :tangle (eval h_func) :noweb yes
|
|
qmckl_exit_code qmckl_get_nucleus_nn_distance_rescaled(qmckl_context context, double* distance_rescaled);
|
|
#+end_src
|
|
|
|
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_get_nucleus_nn_distance_rescaled(qmckl_context context, double* distance_rescaled)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_exit_code rc = qmckl_provide_nn_distance_rescaled(context);
|
|
if (rc != QMCKL_SUCCESS) return rc;
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
size_t sze = ctx->nucleus.num * ctx->nucleus.num;
|
|
memcpy(distance_rescaled, ctx->nucleus.nn_distance_rescaled, sze * sizeof(double));
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
*** Provide :noexport:
|
|
|
|
#+begin_src c :comments org :tangle (eval h_private_func) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nn_distance_rescaled(qmckl_context context);
|
|
#+end_src
|
|
|
|
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nn_distance_rescaled(qmckl_context context)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
if (!ctx->nucleus.provided) return QMCKL_NOT_PROVIDED;
|
|
|
|
/* Allocate array */
|
|
if (ctx->nucleus.nn_distance_rescaled == NULL) {
|
|
|
|
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
|
|
mem_info.size = ctx->nucleus.num * ctx->nucleus.num * sizeof(double);
|
|
double* nn_distance_rescaled = (double*) qmckl_malloc(context, mem_info);
|
|
|
|
if (nn_distance_rescaled == NULL) {
|
|
return qmckl_failwith( context,
|
|
QMCKL_ALLOCATION_FAILED,
|
|
"qmckl_nn_distance_rescaled",
|
|
NULL);
|
|
}
|
|
ctx->nucleus.nn_distance_rescaled = nn_distance_rescaled;
|
|
}
|
|
|
|
qmckl_exit_code rc =
|
|
qmckl_compute_nn_distance_rescaled(context,
|
|
ctx->nucleus.num,
|
|
ctx->nucleus.rescale_factor_kappa,
|
|
ctx->nucleus.coord,
|
|
ctx->nucleus.nn_distance_rescaled);
|
|
if (rc != QMCKL_SUCCESS) {
|
|
return rc;
|
|
}
|
|
|
|
ctx->nucleus.nn_distance_rescaled_date = ctx->date;
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
*** Compute
|
|
|
|
#+NAME: qmckl_nn_distance_rescaled_args
|
|
| qmckl_context | context | in | Global state |
|
|
| int64_t | nucl_num | in | Number of nuclei |
|
|
| double | coord[3][nucl_num] | in | Nuclear coordinates (au) |
|
|
| double | nn_distance_rescaled[nucl_num][nucl_num] | out | Nucleus-nucleus rescaled distances (au) |
|
|
|
|
#+begin_src f90 :comments org :tangle (eval f) :noweb yes
|
|
integer function qmckl_compute_nn_distance_rescaled_f(context, nucl_num, rescale_factor_kappa, coord, nn_distance_rescaled) &
|
|
result(info)
|
|
use qmckl
|
|
implicit none
|
|
integer(qmckl_context), intent(in) :: context
|
|
integer*8 , intent(in) :: nucl_num
|
|
double precision , intent(in) :: rescale_factor_kappa
|
|
double precision , intent(in) :: coord(nucl_num,3)
|
|
double precision , intent(out) :: nn_distance_rescaled(nucl_num,nucl_num)
|
|
|
|
integer*8 :: k
|
|
|
|
info = QMCKL_SUCCESS
|
|
|
|
if (context == QMCKL_NULL_CONTEXT) then
|
|
info = QMCKL_INVALID_CONTEXT
|
|
return
|
|
endif
|
|
|
|
if (nucl_num <= 0) then
|
|
info = QMCKL_INVALID_ARG_2
|
|
return
|
|
endif
|
|
|
|
info = qmckl_distance_rescaled(context, 'T', 'T', nucl_num, nucl_num, &
|
|
coord, nucl_num, &
|
|
coord, nucl_num, &
|
|
nn_distance_rescaled, nucl_num, rescale_factor_kappa)
|
|
|
|
end function qmckl_compute_nn_distance_rescaled_f
|
|
#+end_src
|
|
|
|
#+begin_src c :tangle (eval h_private_func) :comments org :exports none
|
|
qmckl_exit_code qmckl_compute_nn_distance_rescaled (
|
|
const qmckl_context context,
|
|
const int64_t nucl_num,
|
|
const double rescale_factor_kappa,
|
|
const double* coord,
|
|
double* const nn_distance_rescaled );
|
|
#+end_src
|
|
|
|
|
|
#+CALL: generate_c_interface(table=qmckl_nn_distance_rescaled_args,rettyp="qmckl_exit_code",fname="qmckl_compute_nn_distance")
|
|
|
|
#+RESULTS:
|
|
#+begin_src f90 :tangle (eval f) :comments org :exports none
|
|
integer(c_int32_t) function qmckl_compute_nn_distance_rescaled &
|
|
(context, nucl_num, rescale_factor_kappa, coord, nn_distance_rescaled) &
|
|
bind(C) result(info)
|
|
|
|
use, intrinsic :: iso_c_binding
|
|
implicit none
|
|
|
|
integer (c_int64_t) , intent(in) , value :: context
|
|
integer (c_int64_t) , intent(in) , value :: nucl_num
|
|
real (c_double ) , intent(in) , value :: rescale_factor_kappa
|
|
real (c_double ) , intent(in) :: coord(nucl_num,3)
|
|
real (c_double ) , intent(out) :: nn_distance_rescaled(nucl_num,nucl_num)
|
|
|
|
integer(c_int32_t), external :: qmckl_compute_nn_distance_rescaled_f
|
|
info = qmckl_compute_nn_distance_rescaled_f &
|
|
(context, nucl_num, rescale_factor_kappa, coord, nn_distance_rescaled)
|
|
|
|
end function qmckl_compute_nn_distance_rescaled
|
|
#+end_src
|
|
|
|
*** Test
|
|
|
|
#+begin_src c :tangle (eval c_test)
|
|
/* Reference input data */
|
|
/* TODO */
|
|
|
|
//assert(qmckl_nucleus_provided(context));
|
|
//
|
|
//double distance[nucl_num*nucl_num];
|
|
//rc = qmckl_get_nucleus_nn_distance(context, distance);
|
|
//assert(distance[0] == 0.);
|
|
//assert(distance[1] == distance[nucl_num]);
|
|
//assert(fabs(distance[1]-2.070304721365169) < 1.e-12);
|
|
|
|
#+end_src
|
|
|
|
** Nuclear repulsion energy
|
|
|
|
\[
|
|
V_{NN} = \sum_{A=1}^{N-1} \sum_{B>A}^N \frac{Q_A Q_B}{R_{AB}}
|
|
\]
|
|
|
|
*** Get
|
|
|
|
#+begin_src c :comments org :tangle (eval h_func) :noweb yes
|
|
qmckl_exit_code qmckl_get_nucleus_repulsion(qmckl_context context, double* energy);
|
|
#+end_src
|
|
|
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#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_get_nucleus_repulsion(qmckl_context context, double* energy)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_exit_code rc = qmckl_provide_nucleus_repulsion(context);
|
|
if (rc != QMCKL_SUCCESS) return rc;
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
*energy = ctx->nucleus.repulsion;
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
|
|
interface
|
|
integer(c_int32_t) function qmckl_get_nucleus_repulsion(context, energy) &
|
|
bind(C)
|
|
use, intrinsic :: iso_c_binding
|
|
import
|
|
implicit none
|
|
integer (c_int64_t) , intent(in) , value :: context
|
|
real (c_double ) , intent(out) :: energy
|
|
end function
|
|
end interface
|
|
#+end_src
|
|
|
|
*** Provide :noexport:
|
|
|
|
#+begin_src c :comments org :tangle (eval h_private_func) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nucleus_repulsion(qmckl_context context);
|
|
#+end_src
|
|
|
|
#+begin_src c :comments org :tangle (eval c) :noweb yes :exports none
|
|
qmckl_exit_code qmckl_provide_nucleus_repulsion(qmckl_context context)
|
|
{
|
|
/* Check input parameters */
|
|
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
|
|
return (char) 0;
|
|
}
|
|
|
|
qmckl_context_struct* const ctx = (qmckl_context_struct* const) context;
|
|
assert (ctx != NULL);
|
|
|
|
qmckl_exit_code rc;
|
|
|
|
if (!ctx->nucleus.provided) return QMCKL_NOT_PROVIDED;
|
|
|
|
rc = qmckl_provide_nn_distance(context);
|
|
if (rc != QMCKL_SUCCESS) return rc;
|
|
|
|
rc = qmckl_compute_nucleus_repulsion(context,
|
|
ctx->nucleus.num,
|
|
ctx->nucleus.charge,
|
|
ctx->nucleus.nn_distance,
|
|
&(ctx->nucleus.repulsion));
|
|
if (rc != QMCKL_SUCCESS) {
|
|
return rc;
|
|
}
|
|
|
|
ctx->nucleus.repulsion_date = ctx->date;
|
|
|
|
return QMCKL_SUCCESS;
|
|
}
|
|
#+end_src
|
|
|
|
*** Compute
|
|
|
|
#+NAME: qmckl_nucleus_repulsion_args
|
|
| qmckl_context | context | in | Global state |
|
|
| int64_t | nucl_num | in | Number of nuclei |
|
|
| double | charge[nucl_num] | in | Nuclear charges (au) |
|
|
| double | nn_distance[nucl_num][nucl_num] | in | Nucleus-nucleus distances (au) |
|
|
| double | energy | out | Nuclear repulsion energy |
|
|
|
|
#+begin_src f90 :comments org :tangle (eval f) :noweb yes
|
|
integer function qmckl_compute_nucleus_repulsion_f(context, nucl_num, charge, nn_distance, energy) &
|
|
result(info)
|
|
use qmckl
|
|
implicit none
|
|
integer(qmckl_context), intent(in) :: context
|
|
integer*8 , intent(in) :: nucl_num
|
|
double precision , intent(in) :: charge(nucl_num)
|
|
double precision , intent(in) :: nn_distance(nucl_num,nucl_num)
|
|
double precision , intent(out) :: energy
|
|
|
|
integer*8 :: i, j
|
|
|
|
info = QMCKL_SUCCESS
|
|
|
|
if (context == QMCKL_NULL_CONTEXT) then
|
|
info = QMCKL_INVALID_CONTEXT
|
|
return
|
|
endif
|
|
|
|
if (nucl_num <= 0) then
|
|
info = QMCKL_INVALID_ARG_2
|
|
return
|
|
endif
|
|
|
|
energy = 0.d0
|
|
do j=2, nucl_num
|
|
do i=1, j-1
|
|
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
|
|
end do
|
|
end do
|
|
|
|
end function qmckl_compute_nucleus_repulsion_f
|
|
#+end_src
|
|
|
|
#+begin_src c :tangle (eval h_private_func) :comments org :exports none
|
|
qmckl_exit_code qmckl_compute_nucleus_repulsion (
|
|
const qmckl_context context,
|
|
const int64_t nucl_num,
|
|
const double* charge,
|
|
const double* nn_distance,
|
|
double* energy
|
|
);
|
|
#+end_src
|
|
|
|
#+CALL: generate_c_interface(table=qmckl_nucleus_repulsion_args,rettyp="qmckl_exit_code",fname="qmckl_compute_nucleus_repulsion")
|
|
|
|
#+RESULTS:
|
|
#+begin_src f90 :tangle (eval f) :comments org :exports none
|
|
integer(c_int32_t) function qmckl_compute_nucleus_repulsion &
|
|
(context, nucl_num, charge, nn_distance, energy) &
|
|
bind(C) result(info)
|
|
|
|
use, intrinsic :: iso_c_binding
|
|
implicit none
|
|
|
|
integer (c_int64_t) , intent(in) , value :: context
|
|
integer (c_int64_t) , intent(in) , value :: nucl_num
|
|
real (c_double ) , intent(in) :: charge(nucl_num)
|
|
real (c_double ) , intent(in) :: nn_distance(nucl_num,nucl_num)
|
|
real (c_double ) , intent(out) :: energy
|
|
|
|
integer(c_int32_t), external :: qmckl_compute_nucleus_repulsion_f
|
|
info = qmckl_compute_nucleus_repulsion_f &
|
|
(context, nucl_num, charge, nn_distance, energy)
|
|
|
|
end function qmckl_compute_nucleus_repulsion
|
|
#+end_src
|
|
|
|
*** Test
|
|
|
|
#+begin_src c :tangle (eval c_test)
|
|
/* Reference input data */
|
|
|
|
assert(qmckl_nucleus_provided(context));
|
|
|
|
double rep;
|
|
rc = qmckl_get_nucleus_repulsion(context, &rep);
|
|
assert(rep - 318.2309879436158 < 1.e-10);
|
|
|
|
#+end_src
|
|
|
|
* End of files :noexport:
|
|
|
|
#+begin_src c :tangle (eval h_private_type)
|
|
#endif
|
|
#+end_src
|
|
|
|
*** Test
|
|
#+begin_src c :tangle (eval c_test)
|
|
if (qmckl_context_destroy(context) != QMCKL_SUCCESS)
|
|
return QMCKL_FAILURE;
|
|
return 0;
|
|
}
|
|
#+end_src
|
|
|
|
*** Compute file names
|
|
#+begin_src emacs-lisp
|
|
; The following is required to compute the file names
|
|
|
|
(setq pwd (file-name-directory buffer-file-name))
|
|
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
|
(setq f (concat pwd name "_f.f90"))
|
|
(setq fh (concat pwd name "_fh.f90"))
|
|
(setq c (concat pwd name ".c"))
|
|
(setq h (concat name ".h"))
|
|
(setq h_private (concat name "_private.h"))
|
|
(setq c_test (concat pwd "test_" name ".c"))
|
|
(setq f_test (concat pwd "test_" name "_f.f90"))
|
|
|
|
; Minted
|
|
(require 'ox-latex)
|
|
(setq org-latex-listings 'minted)
|
|
(add-to-list 'org-latex-packages-alist '("" "listings"))
|
|
(add-to-list 'org-latex-packages-alist '("" "color"))
|
|
|
|
#+end_src
|
|
|
|
#+RESULTS:
|
|
|
|
|
|
# -*- mode: org -*-
|
|
# vim: syntax=c
|
|
|
|
|