From b8391b11c2fcbd42c39ab6e95971d01d12a0c872 Mon Sep 17 00:00:00 2001 From: scemama Date: Wed, 12 May 2021 11:36:57 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20TREX-CoE?= =?UTF-8?q?/qmckl@0fdaea77c954ad6582bfceff9ef4fe488b8bdd43=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.html | 4 +- qmckl.html | 102 ++++++++++++++-------------- qmckl_ao.html | 158 ++++++++++++++++++++++---------------------- qmckl_context.html | 44 ++++++------ qmckl_distance.html | 80 +++++++++++----------- qmckl_electron.html | 66 +++++++++--------- qmckl_error.html | 28 ++++---- qmckl_memory.html | 22 +++--- qmckl_numprec.html | 30 ++++----- 9 files changed, 267 insertions(+), 267 deletions(-) diff --git a/README.html b/README.html index fdfe591..4cf9227 100644 --- a/README.html +++ b/README.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + QMCkl source code documentation @@ -349,7 +349,7 @@ and bug reports should be submitted at

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl.html b/qmckl.html index 0d03053..2f32cfb 100644 --- a/qmckl.html +++ b/qmckl.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Introduction @@ -333,30 +333,30 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Using QMCkl

+
+

1 Using QMCkl

The qmckl.h header file installed in the ${prefix}/include directory @@ -385,12 +385,12 @@ Both files are located in the include/ directory.

-
-

2 Developing in QMCkl

+
+

2 Developing in QMCkl

-
-

2.1 Literate programming

+
+

2.1 Literate programming

In a traditional source code, most of the lines of source files of a program @@ -435,8 +435,8 @@ interactively, in the same spirit as Jupyter notebooks.

-
-

2.2 Source code editing

+
+

2.2 Source code editing

For a tutorial on literate programming with org-mode, follow this link. @@ -467,8 +467,8 @@ org-mode.

-
-

2.3 Choice of the programming language

+
+

2.3 Choice of the programming language

Most of the codes of the TREX CoE are written in Fortran with some scripts in @@ -516,8 +516,8 @@ For more guidelines on using Fortran to generate a C interface, see

-
-

2.4 Coding rules

+
+

2.4 Coding rules

The authors should follow the recommendations of the C99 @@ -535,8 +535,8 @@ Compliance can be checked with cppcheck as:

-
-

2.5 Design of the library

+
+

2.5 Design of the library

The proposed API should allow the library to: deal with memory transfers @@ -547,8 +547,8 @@ functions (see below).

-
-

2.6 Naming conventions

+
+

2.6 Naming conventions

To avoid namespace collisions, we use qmckl_ as a prefix for all exported @@ -573,8 +573,8 @@ form is allowed.

-
-

2.7 Application programming interface

+
+

2.7 Application programming interface

In the C language, the number of bits used by the integer types can change @@ -606,15 +606,15 @@ bindings in other languages in other repositories.

-
-

2.8 Global state

+
+

2.8 Global state

Global variables should be avoided in the library, because it is possible that one single program needs to use multiple instances of the library. To solve this problem we propose to use a pointer to a context variable, built by the library with the -qmckl_context_create function. The =context= contains the global +qmckl_context_create function. The =context= contains the global state of the library, and is used as the first argument of many QMCkl functions.

@@ -628,8 +628,8 @@ the state is done by setters and getters, prefixed by
-
-

2.9 Headers

+
+

2.9 Headers

A single qmckl.h header to be distributed by the library @@ -717,8 +717,8 @@ and the types definitions should be written in the *_f_type.f90 fil

-
-

2.10 Low-level functions

+
+

2.10 Low-level functions

Low-level functions are very simple functions which are leaves of @@ -727,14 +727,14 @@ the function call tree (they don't call any other QMCkl function).

These functions are pure, and unaware of the QMCkl -context. They are not allowed to allocate/deallocate memory, and +context. They are not allowed to allocate/deallocate memory, and if they need temporary memory it should be provided in input.

-
-

2.11 High-level functions

+
+

2.11 High-level functions

High-level functions are at the top of the function call tree. @@ -747,27 +747,27 @@ temporary storage, to simplify the use of accelerators.

The high-level functions should be pure, unless the introduction of non-purity is justified. All the side effects should be made in -the context variable. +the context variable.

-
-

2.12 Numerical precision

+
+

2.12 Numerical precision

The number of bits of precision required for a function should be given as an input of low-level computational functions. This input will be used to define the values of the different thresholds that might be used to avoid computing unnecessary noise. High-level -functions will use the precision specified in the context +functions will use the precision specified in the context variable.

-
-

2.13 Algorithms

+
+

2.13 Algorithms

Reducing the scaling of an algorithm usually implies also reducing @@ -783,7 +783,7 @@ implemented adapted to different problem sizes.

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_ao.html b/qmckl_ao.html index d94568b..8ceaf99 100644 --- a/qmckl_ao.html +++ b/qmckl_ao.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Atomic Orbitals @@ -333,52 +333,52 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Context

+
+

1 Context

The following arrays are stored in the context: @@ -503,8 +503,8 @@ coefficient = [ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421,

-
-

1.1 Data structure

+
+

1.1 Data structure

typedef struct qmckl_ao_basis_struct {
@@ -533,8 +533,8 @@ struct is then initialized and provided == true.
-
-

1.2 Access functions

+
+

1.2 Access functions

When all the data for the AOs have been provided, the following @@ -548,8 +548,8 @@ function returns true.

-
-

1.3 Initialization functions

+
+

1.3 Initialization functions

To set the basis set, all the following functions need to be @@ -572,17 +572,17 @@ called. When

-
-

1.4 TODO Fortran interfaces

+
+

1.4 TODO Fortran interfaces

-
-

2 Polynomial part

+
+

2 Polynomial part

-
-

2.1 Powers of \(x-X_i\)

+
+

2.1 Powers of \(x-X_i\)

The qmckl_ao_power function computes all the powers of the n @@ -594,7 +594,7 @@ the \(n\) points: \[ P_{ik} = X_i^k \]

- +
@@ -652,8 +652,8 @@ the \(n\) points:
-
-

2.1.1 Requirements

+
+

2.1.1 Requirements

  • context is not QMCKL_NULL_CONTEXT
    • @@ -666,8 +666,8 @@ the \(n\) points:
-
-

2.1.2 C Header

+
+

2.1.2 C Header

qmckl_exit_code qmckl_ao_power (
@@ -682,8 +682,8 @@ the \(n\) points:
-
-

2.1.3 Source

+
+

2.1.3 Source

integer function qmckl_ao_power_f(context, n, X, LMAX, P, ldp) result(info)
@@ -734,15 +734,15 @@ the \(n\) points:
-
-

2.1.4 C interface

+
+

2.1.4 C interface

-
-

2.1.5 Fortran interface

+
+

2.1.5 Fortran interface

-
-

2.1.6 Test

+
+

2.1.6 Test

integer(c_int32_t) function test_qmckl_ao_power(context) bind(C)
@@ -793,8 +793,8 @@ the \(n\) points:
-
-

2.2 Value, Gradient and Laplacian of a polynomial

+
+

2.2 Value, Gradient and Laplacian of a polynomial

A polynomial is centered on a nucleus \(\mathbf{R}_i\) @@ -839,7 +839,7 @@ Laplacians at a given point in space, of all polynomials with an angular momentum up to lmax.

- +
@@ -918,8 +918,8 @@ angular momentum up to lmax.
-
-

2.2.1 Requirements

+
+

2.2.1 Requirements

  • context is not QMCKL_NULL_CONTEXT
    • @@ -944,8 +944,8 @@ For example, with a=0, b=2 and c=1 the string is "yyz"
-
-

2.2.2 C Header

+
+

2.2.2 C Header

qmckl_exit_code qmckl_ao_polynomial_vgl (
@@ -963,8 +963,8 @@ For example, with a=0, b=2 and c=1 the string is "yyz"
-
-

2.2.3 Source

+
+

2.2.3 Source

integer function qmckl_ao_polynomial_vgl_f(context, X, R, lmax, n, L, ldl, VGL, ldv) result(info)
@@ -1099,16 +1099,16 @@ For example, with a=0, b=2 and c=1 the string is "yyz"
-
-

2.2.4 C interface

+
+

2.2.4 C interface

-
-

2.2.5 Fortran interface

+
+

2.2.5 Fortran interface

-
-

2.2.6 Test

+
+

2.2.6 Test

integer(c_int32_t) function test_qmckl_ao_polynomial_vgl(context) bind(C)
@@ -1213,12 +1213,12 @@ assert(0 == test_qmckl_ao_polynomial_vgl(context));
-
-

3 Radial part

+
+

3 Radial part

-
-

3.1 Gaussian basis functions

+
+

3.1 Gaussian basis functions

qmckl_ao_gaussian_vgl computes the values, gradients and @@ -1450,21 +1450,21 @@ Requirements

-
-

3.2 TODO Slater basis functions

+
+

3.2 TODO Slater basis functions

-
-

3.3 TODO Radial functions on a grid

+
+

3.3 TODO Radial functions on a grid

-
-

4 Combining radial and polynomial parts

+
+

4 Combining radial and polynomial parts

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_context.html b/qmckl_context.html index 8d10744..030ba4c 100644 --- a/qmckl_context.html +++ b/qmckl_context.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Context @@ -311,21 +311,21 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Context handling

+
+

1 Context handling

The context variable is a handle for the state of the library, @@ -338,7 +338,7 @@ A value of QMCKL_NULL_CONTEXT for the context is equivalent to a

-
typedef int64_t qmckl_context ;
+
typedef int64_t qmckl_context ;
 #define QMCKL_NULL_CONTEXT (qmckl_context) 0
@@ -356,8 +356,8 @@ and ctx is a qmckl_context_struct* pointer.

-
-

1.1 Data structure

+
+

1.1 Data structure

The context keeps a ``date'' that allows to check which data needs @@ -367,7 +367,7 @@ coordinates are updated.

When a new element is added to the context, the functions -qmcklcontextcreate, qmcklcontextdestroy and qmcklcontextcopy +qmcklcontextcreate, qmcklcontextdestroy and qmcklcontextcopy should be updated inorder to make deep copies.

@@ -416,8 +416,8 @@ if the context is valid, QMCKL_NULL_CONTEXT otherwise.
-
-

1.2 Creation

+
+

1.2 Creation

To create a new context, qmckl_context_create() should be used. @@ -491,8 +491,8 @@ To create a new context, qmckl_context_create() should be used.

-
-

1.3 Locking

+
+

1.3 Locking

For thread safety, the context may be locked/unlocked. The lock is @@ -537,8 +537,8 @@ number of times the thread has locked it is saved in the

-
-

1.4 TODO Copy

+
+

1.4 TODO Copy

qmckl_context_copy makes a deep copy of a context. It returns @@ -586,8 +586,8 @@ number of times the thread has locked it is saved in the

-
-

1.5 Destroy

+
+

1.5 Destroy

The context is destroyed with qmckl_context_destroy, leaving the ancestors untouched. @@ -641,7 +641,7 @@ It frees the context, and returns the previous context.

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_distance.html b/qmckl_distance.html index e78bd37..75f2494 100644 --- a/qmckl_distance.html +++ b/qmckl_distance.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Inter-particle distances @@ -333,26 +333,26 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Squared distance

+
+

1 Squared distance

-
-

1.1 qmckl_distance_sq

+
+

1.1 qmckl_distance_sq

qmckl_distance_sq computes the matrix of the squared distances @@ -379,7 +379,7 @@ between all pairs of points in two sets, one point within each set: \]

- +
@@ -472,8 +472,8 @@ between all pairs of points in two sets, one point within each set:
-
-

1.1.1 Requirements

+
+

1.1.1 Requirements

  • context is not QMCKL_NULL_CONTEXT
    • @@ -491,8 +491,8 @@ between all pairs of points in two sets, one point within each set:
-
-

1.1.2 C header

+
+

1.1.2 C header

qmckl_exit_code qmckl_distance (
@@ -512,8 +512,8 @@ between all pairs of points in two sets, one point within each set:
-
-

1.1.3 Source

+
+

1.1.3 Source

integer function qmckl_distance_sq_f(context, transa, transb, m, n, &
@@ -648,8 +648,8 @@ between all pairs of points in two sets, one point within each set:
-
-

1.1.4 Performance

+
+

1.1.4 Performance

This function might be more efficient when A and B are @@ -659,12 +659,12 @@ transposed.

-
-

2 Distance

+
+

2 Distance

-
-

2.1 qmckl_distance

+
+

2.1 qmckl_distance

qmckl_distance computes the matrix of the distances between all @@ -677,7 +677,7 @@ pairs of points in two sets, one point within each set: \]

- +
@@ -770,8 +770,8 @@ pairs of points in two sets, one point within each set:
-
-

2.1.1 Requirements

+
+

2.1.1 Requirements

  • context is not QMCKL_NULL_CONTEXT
    • @@ -789,8 +789,8 @@ pairs of points in two sets, one point within each set:
-
-

2.1.2 C header

+
+

2.1.2 C header

qmckl_exit_code qmckl_distance (
@@ -810,8 +810,8 @@ pairs of points in two sets, one point within each set:
-
-

2.1.3 Source

+
+

2.1.3 Source

integer function qmckl_distance_f(context, transa, transb, m, n, &
@@ -950,8 +950,8 @@ pairs of points in two sets, one point within each set:
-
-

2.1.4 Performance

+
+

2.1.4 Performance

This function might be more efficient when A and B are @@ -964,7 +964,7 @@ transposed.

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_electron.html b/qmckl_electron.html index cfc87f2..0f7f458 100644 --- a/qmckl_electron.html +++ b/qmckl_electron.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Electrons @@ -311,21 +311,21 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Context

+
+

1 Context

The following data stored in the context: @@ -421,8 +421,8 @@ The following data stored in the context:

-
-

1.1 Data structure

+
+

1.1 Data structure

typedef struct qmckl_electron_struct {
@@ -450,8 +450,8 @@ struct is then initialized and provided == true.
-
-

1.2 Access functions

+
+

1.2 Access functions

When all the data relative to electrons have been set, the @@ -465,8 +465,8 @@ following function returns true.

-
-

1.3 Initialization functions

+
+

1.3 Initialization functions

To set the data relative to the electrons in the context, the @@ -496,8 +496,8 @@ electrons have been set.

-
-

1.4 Test

+
+

1.4 Test

/* Reference input data */
@@ -542,8 +542,8 @@ rc = qmckl_set_electron_coord (context, coord);
-
-

2 Computation

+
+

2 Computation

The computed data is stored in the context so that it can be reused @@ -556,12 +556,12 @@ current date is stored.

-
-

2.1 Electron-electron distances

+
+

2.1 Electron-electron distances

-
-

2.1.1 Get

+
+

2.1.1 Get

qmckl_exit_code qmckl_get_electron_ee_distance(qmckl_context context, double* distance);
@@ -570,10 +570,10 @@ current date is stored.
-
-

2.1.2 Compute

+
+

2.1.2 Compute

- +
@@ -670,8 +670,8 @@ current date is stored. -
-

2.1.3 Test

+
+

2.1.3 Test

/* Reference input data */
@@ -694,7 +694,7 @@ rc = qmckl_get_electron_ee_distance(context, distance);

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_error.html b/qmckl_error.html index 7a6780f..abba2fe 100644 --- a/qmckl_error.html +++ b/qmckl_error.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Error handling @@ -311,16 +311,16 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Decoding errors

+
+

1 Decoding errors

To decode the error messages, qmckl_string_of_error converts an @@ -414,8 +414,8 @@ The text strings are extracted from the previous table.

-
-

2 Data structure in context

+
+

2 Data structure in context

The strings are declared with a maximum fixed size to avoid @@ -438,8 +438,8 @@ dynamic memory allocation.

-
-

3 Updating errors in the context

+
+

3 Updating errors in the context

The error is updated in the context using qmckl_set_error. @@ -485,8 +485,8 @@ explaining the error. The exit code can't be QMCKL_SUCCESS.

-
-

4 Failing

+
+

4 Failing

To make a function fail, the qmckl_failwith function should be @@ -549,7 +549,7 @@ For example, this function can be used as

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_memory.html b/qmckl_memory.html index 0686370..98ce81c 100644 --- a/qmckl_memory.html +++ b/qmckl_memory.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Memory management @@ -311,15 +311,15 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Memory data structure for the context

+
+

1 Memory data structure for the context

Every time a new block of memory is allocated, the information @@ -361,8 +361,8 @@ array, and the number of allocated blocks.

-
-

2 Passing info to allocation routines

+
+

2 Passing info to allocation routines

Passing information to the allocation routine should be done by @@ -371,8 +371,8 @@ passing an instance of a qmckl_memory_info_struct.

-
-

3 Allocation/deallocation functions

+
+

3 Allocation/deallocation functions

Memory allocation inside the library should be done with @@ -535,7 +535,7 @@ allocation and needs to be updated.

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate

diff --git a/qmckl_numprec.html b/qmckl_numprec.html index b9c9014..744b424 100644 --- a/qmckl_numprec.html +++ b/qmckl_numprec.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Numerical precision @@ -333,16 +333,16 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Control of the numerical precision

+
+

1 Control of the numerical precision

Controlling numerical precision enables optimizations. Here, the @@ -353,7 +353,7 @@ Arithmetic (IEEE 754), refers to the number of exponent bits.

-
+
@@ -397,8 +397,8 @@ integer. The update functions return QMCKL_SUCCESS or -
-

2 Precision

+
+

2 Precision

qmckl_context_set_numprec_precision modifies the parameter for the @@ -485,8 +485,8 @@ numerical precision in the context.

-
-

3 Range

+
+

3 Range

qmckl_set_numprec_range modifies the parameter for the numerical @@ -561,8 +561,8 @@ range in a given context.

-
-

4 Helper functions

+
+

4 Helper functions

qmckl_get_numprec_epsilon returns \(\epsilon = 2^{1-n}\) where n is the precision. @@ -581,7 +581,7 @@ We need to remove the sign bit from the precision.

Author: TREX CoE

-

Created: 2021-05-12 Wed 11:34

+

Created: 2021-05-12 Wed 11:36

Validate