diff --git a/README.html b/README.html index 3bfa37f..5f21c1b 100644 --- a/README.html +++ b/README.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
- +All QMCkl functions return an error code. A convenient way to handle @@ -327,7 +327,7 @@ error in text format and exits the program.
subroutine qmckl_check_error(rc, message) +subroutine qmckl_check_error(rc, message) use qmckl implicit none integer(qmckl_exit_code), intent(in) :: rc @@ -345,8 +345,8 @@ error in text format and exits the program.
The following program, in Fortran, computes the values of an atomic @@ -564,7 +564,7 @@ We finally print the value of the AO:
The latest version fo QMCkl can be downloaded @@ -371,8 +371,8 @@ The latest version fo QMCkl can be downloaded
QMCkl is built with GNU Autotools, so the usual
@@ -387,8 +387,8 @@ options are defined using CFLAGS
and FCFLAGS
.
To compile from the source repository, additional dependencies are @@ -409,8 +409,8 @@ to be executed first.
The qmckl.h
header file installed in the ${prefix}/include
directory
@@ -439,12 +439,12 @@ Both files are located in the include/
directory.
In a traditional source code, most of the lines of source files of a program @@ -494,8 +494,8 @@ tarball contains the generated source code.
For a tutorial on literate programming with org-mode, follow this link. @@ -526,8 +526,8 @@ org-mode.
Most of the codes of the TREX CoE are written in Fortran with some @@ -591,8 +591,8 @@ For more guidelines on using Fortran to generate a C interface, see
The authors should follow the recommendations of the C99 @@ -612,8 +612,8 @@ make cppcheck ; cat cppcheck.out
The proposed API should allow the library to: deal with memory transfers @@ -624,8 +624,8 @@ functions (see below).
To avoid namespace collisions, we use qmckl_
as a prefix for all exported
@@ -646,8 +646,8 @@ form is allowed.
In the C language, the number of bits used by the integer types can change @@ -679,15 +679,15 @@ bindings in other languages in other repositories.
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.
A single qmckl.h
header to be distributed by the library
@@ -790,8 +790,8 @@ and the types definitions should be written in the *fh_type.f90
fil
Low-level functions are very simple functions which are leaves of @@ -800,14 +800,14 @@ 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.
High-level functions are at the top of the function call tree. @@ -819,8 +819,8 @@ temporary storage, to simplify the use of accelerators.
The minimal number of bits of precision required for a function
@@ -828,7 +828,7 @@ 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
variable.
+specified in the context
variable.
@@ -896,8 +896,8 @@ following points :
Reducing the scaling of an algorithm usually implies also reducing @@ -913,7 +913,7 @@ implemented adapted to different problem sizes.
The atomic basis set is defined as a list of shells. Each shell \(s\) is @@ -439,19 +439,19 @@ gradients and Laplacian of the atomic basis functions.
The following arrays are stored in the context, and need to be set when initializing the library:
-When the basis set is completely entered, extra data structures may be @@ -1414,8 +1414,8 @@ the context.
For faster access, we provide extra arrays for the shell information as: @@ -1445,8 +1445,8 @@ which is a matrix-vector product.
qmckl_exit_code @@ -1459,7 +1459,7 @@ which is a matrix-vector product.Returns the array of values, gradients an Laplacian of primitive basis functions evaluated at the current coordinates. -See section 3.2. +See section 3.2.
@@ -1472,7 +1472,7 @@ See section 3.2.-Returns the array of values, gradients an Laplacian of contracted shells -evaluated at the current coordinates. See section 3.3. +evaluated at the current coordinates. See section 3.3.
-3 Radial part
++3 Radial part
--3.1 General functions for Gaussian basis functions
++-3.1 General functions for Gaussian basis functions
qmckl_ao_gaussian_vgl
computes the values, gradients and @@ -1681,10 +1681,10 @@ Requirements:-3.2 Computation of primitives
++3.2 Computation of primitives
-+
@@ -1843,10 +1843,10 @@ Requirements: - -3.3 Computation of shells
++3.3 Computation of shells
-+
@@ -2098,8 +2098,8 @@ Requirements: - -4 Polynomial part
++4 Polynomial part
-Going from the atomic basis set to AOs implies a systematic @@ -2119,8 +2119,8 @@ f & : & f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}, f_{xzz}, f_{yyy}, f_{yyz}, \end{eqnarray}
-4.1 General functions for Powers of \(x-X_i\)
++4.1 General functions for Powers of \(x-X_i\)
The
-qmckl_ao_power
function computes all the powers of then
@@ -2132,7 +2132,7 @@ the \(n\) points: \[ P_{ik} = X_i^k \]+
@@ -2270,8 +2270,8 @@ Requirements: - -4.2 General functions for Value, Gradient and Laplacian of a polynomial
++4.2 General functions for Value, Gradient and Laplacian of a polynomial
A polynomial is centered on a nucleus \(\mathbf{R}_i\) @@ -2316,7 +2316,7 @@ Laplacians at a given point in space, of all polynomials with an angular momentum up to
-lmax
.+
@@ -3080,15 +3080,15 @@ For example, with a=0, b=2 and c=1 the string is "yyz" - -5 Combining radial and polynomial parts
++5 Combining radial and polynomial parts
--5.1 Unoptimized version
++5.1 Unoptimized version
-+
@@ -3353,10 +3353,10 @@ For example, with a=0, b=2 and c=1 the string is "yyz" - -5.2 HPC version
++5.2 HPC version
-+
@@ -3515,8 +3515,8 @@ For example, with a=0, b=2 and c=1 the string is "yyz" - -5.3 Interfaces
++5.3 Interfaces
-diff --git a/qmckl_blas.html b/qmckl_blas.html index c14a2ec..a0b100b 100644 --- a/qmckl_blas.html +++ b/qmckl_blas.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + -qmckl_exit_code qmckl_compute_ao_vgl_doc ( @@ -3566,7 +3566,7 @@ For example, with a=0, b=2 and c=1 the string is "yyz"BLAS functions @@ -333,48 +333,48 @@ for the JavaScript code in this tag.Table of Contents
-
- -
-- 1. Data types +
- -
+- 1. Data types
-- 2. Matrix operations +
- 2. Matrix operations
--
-++--
+Basic linear algebra data types and operations are described in this file. The data types are private, so that HPC implementations can use @@ -388,12 +388,12 @@ are not intended to be passed to external codes.
-1 Data types
++1 Data types
--1.1 Vector
++1.1 Vector
@@ -447,8 +447,8 @@ Allocates a new vector. If the allocation failed the size is zero. -
-1.2 Matrix
++1.2 Matrix
@@ -508,8 +508,8 @@ Allocates a new matrix. If the allocation failed the sizes are zero. -
-1.3 Tensor
++1.3 Tensor
@@ -576,16 +576,16 @@ is zero. -
-1.4 Reshaping
++1.4 Reshaping
-Reshaping occurs in-place and the pointer to the data is copied.
-1.4.1 Vector -> Matrix
++1.4.1 Vector -> Matrix
-qmckl_matrix @@ -601,8 +601,8 @@ Reshapes a vector into a matrix.
-1.4.2 Vector -> Tensor
++1.4.2 Vector -> Tensor
-qmckl_tensor @@ -618,8 +618,8 @@ Reshapes a vector into a tensor.
-1.4.3 Matrix -> Vector
++1.4.3 Matrix -> Vector
-qmckl_vector @@ -633,8 +633,8 @@ Reshapes a matrix into a vector.
-1.4.4 Matrix -> Tensor
++1.4.4 Matrix -> Tensor
-qmckl_tensor @@ -650,8 +650,8 @@ Reshapes a matrix into a tensor.
-1.4.5 Tensor -> Vector
++1.4.5 Tensor -> Vector
-qmckl_vector @@ -665,8 +665,8 @@ Reshapes a tensor into a vector.
-1.4.6 Tensor -> Matrix
++1.4.6 Tensor -> Matrix
-qmckl_matrix @@ -683,8 +683,8 @@ Reshapes a tensor into a vector.
-1.5 Access macros
++-1.5 Access macros
Macros are provided to ease the access to vectors, matrices and @@ -708,12 +708,12 @@ For example:
-1.6 Set all elements
++1.6 Set all elements
--1.6.1 Vector
++1.6.1 Vector
-qmckl_vector @@ -723,8 +723,8 @@ For example:
-1.6.2 Matrix
++1.6.2 Matrix
-qmckl_matrix @@ -734,8 +734,8 @@ For example:
-1.6.3 Tensor
++1.6.3 Tensor
-qmckl_tensor @@ -746,8 +746,8 @@ For example:
-1.7 Copy to/from to
+double*
+1.7 Copy to/from to
double*
-qmckl_exit_code @@ -830,12 +830,12 @@ Converts adouble*
to a tensor.-2 Matrix operations
++2 Matrix operations
--2.1
+qmckl_dgemm
+2.1
qmckl_dgemm
Matrix multiplication with a BLAS interface: @@ -847,7 +847,7 @@ Matrix multiplication with a BLAS interface: \]
-+
@@ -1006,8 +1006,8 @@ Requirements: - -2.2
+qmckl_matmul
+2.2
qmckl_matmul
Matrix multiplication using the
-qmckl_matrix
data type: @@ -1019,7 +1019,7 @@ Matrix multiplication using theqmckl_matrix
data type: \]+
@@ -1113,8 +1113,8 @@ Matrix multiplication using the qmckl_matrix
data type: --2.3
+qmckl_adjugate
+2.3
qmckl_adjugate
Given a matrix \(\mathbf{A}\), the adjugate matrix @@ -1132,7 +1132,7 @@ of \(\mathbf{A}\). See also: https://en.wikipedia.org/wiki/Adjugate_matrix
-+
-
@@ -1328,8 +1328,8 @@ determinant with the inverse: - -2.4
+qmckl_transpose
+-2.4
qmckl_transpose
diff --git a/qmckl_context.html b/qmckl_context.html index f40b5e4..f30e410 100644 --- a/qmckl_context.html +++ b/qmckl_context.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + -Transposes a matrix: \(A^\dagger_{ji} = A_{ij}\). @@ -1392,7 +1392,7 @@ Transposes a matrix: \(A^\dagger_{ji} = A_{ij}\).
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-@@ -356,8 +356,8 @@ andtypedef int64_t qmckl_context ; +typedef int64_t qmckl_context ; #define QMCKL_NULL_CONTEXT (qmckl_context) 0ctx
is aqmckl_context_struct*
pointer.-1.1 Data structure
++-1.1 Data structure
A tag is used internally to check if the memory domain pointed @@ -385,7 +385,7 @@ to be recomputed. The date is incremented when the context is touched.
When a new element is added to the context, the functions -
@@ -406,8 +406,8 @@ This has the effect to increment the date of the context.qmckl_context_create
qmckl_context_destroy
andqmckl_context_copy
+qmckl_context_create
qmckl_context_destroy
andqmckl_context_copy
should be updated in order to make deep copies.--1.2 Creation
++1.2 Creation
To create a new context,
qmckl_context_create()
should be used. @@ -424,8 +424,8 @@ 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 @@ -441,8 +441,8 @@ 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 @@ -450,8 +450,8 @@ number of times the thread has locked it is saved in the-1.5 Destroy
++-1.5 Destroy
diff --git a/qmckl_determinant.html b/qmckl_determinant.html index c1a3677..78d86a0 100644 --- a/qmckl_determinant.html +++ b/qmckl_determinant.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + -The context is destroyed with
qmckl_context_destroy
, leaving the ancestors untouched. @@ -469,7 +469,7 @@ It frees the context, and returns the previous context.Slater Determinant @@ -311,32 +311,32 @@ for the JavaScript code in this tag.Table of Contents
-
- 1. Context +
- 1. Context
-- 2. Computation +
- 2. Computation @@ -345,8 +345,8 @@ for the JavaScript code in this tag.
-1 Context
++1 Context
The following arrays are stored in the context: @@ -528,8 +528,8 @@ Computed data:
-1.1 Data structure
++1.1 Data structure
-typedef struct qmckl_determinant_struct { @@ -598,8 +598,8 @@ this mechanism.-1.2 Access functions
++-1.2 Access functions
When all the data for the slater determinants have been provided, the following @@ -613,8 +613,8 @@ function returns
true
.-1.3 Initialization functions
++-1.3 Initialization functions
To set the basis set, all the following functions need to be @@ -638,24 +638,24 @@ computed to accelerate the calculations.
-1.4 Fortran Interfaces
++-1.4 Fortran Interfaces
--1.5 Test
++1.5 Test
-2 Computation
++2 Computation
--2.1 Determinant matrix
++2.1 Determinant matrix
--2.1.1 Get
++2.1.1 Get
-qmckl_exit_code qmckl_get_det_vgl_alpha(qmckl_context context, double* const det_vgl_alpha); @@ -665,14 +665,14 @@ computed to accelerate the calculations.-2.1.2 Provide
++-2.1.2 Provide
-2.1.3 Compute alpha
++2.1.3 Compute alpha
-+
@@ -846,10 +846,10 @@ computed to accelerate the calculations. - -2.1.4 Compute beta
++2.1.4 Compute beta
-+
@@ -1023,18 +1023,18 @@ computed to accelerate the calculations. - --2.1.5 Test
++2.1.5 Test
-2.2 Inverse of Determinant matrix
++2.2 Inverse of Determinant matrix
--2.2.1 Get
++2.2.1 Get
-qmckl_exit_code qmckl_get_det_inv_matrix_alpha(qmckl_context context, double* const det_inv_matrix_alpha); @@ -1048,14 +1048,14 @@ computed to accelerate the calculations.-2.2.2 Provide
++-2.2.2 Provide
-2.2.3 Compute alpha
++2.2.3 Compute alpha
-+
@@ -1217,10 +1217,10 @@ computed to accelerate the calculations. - -2.2.4 Compute beta
++2.2.4 Compute beta
-+
@@ -1387,7 +1387,7 @@ computed to accelerate the calculations. diff --git a/qmckl_distance.html b/qmckl_distance.html index d9604a2..5e3f3c2 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 @@ -333,54 +333,54 @@ 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 @@ -393,7 +393,7 @@ between all pairs of points in two sets, one point within each set: \]+
@@ -659,8 +659,8 @@ Requirements: - --1.1.1 Performance
++1.1.1 Performance
This function is more efficient when
A
andB
are @@ -670,12 +670,12 @@ transposed.-2 Distance
++2 Distance
--2.1
+qmckl_distance
+2.1
qmckl_distance
-
qmckl_distance
computes the matrix of the distances between all @@ -693,7 +693,7 @@ If the input array is normal ('N'
), the xyz coordinates are in the leading dimension:[n][3]
in C and(3,n)
in Fortran.+
-
@@ -794,8 +794,8 @@ the leading dimension: [n][3]
in C and(3,n)
in Fortra-2.1.1 Requirements
++-2.1.1 Requirements
- @@ -813,8 +813,8 @@ the leading dimension:
context
is notQMCKL_NULL_CONTEXT
[n][3]
in C and(3,n)
in Fortra-2.1.2 C header
++2.1.2 C header
-qmckl_exit_code qmckl_distance ( @@ -834,8 +834,8 @@ the leading dimension:[n][3]
in C and(3,n)
in Fortra-2.1.3 Source
++2.1.3 Source
-integer function qmckl_distance_f(context, transa, transb, m, n, & @@ -1002,8 +1002,8 @@ the leading dimension:[n][3]
in C and(3,n)
in Fortra-2.1.4 Performance
++-2.1.4 Performance
This function is more efficient when
A
andB
are transposed. @@ -1013,12 +1013,12 @@ This function is more efficient whenA
andB
are trans-3 Rescaled Distance
++3 Rescaled Distance
--3.1
+qmckl_distance_rescaled
+3.1
qmckl_distance_rescaled
-
qmckl_distance_rescaled
computes the matrix of the rescaled distances between all @@ -1036,7 +1036,7 @@ If the input array is normal ('N'
), the xyz coordinates are in the leading dimension:[n][3]
in C and(3,n)
in Fortran.+
-
@@ -1144,8 +1144,8 @@ the leading dimension: [n][3]
in C and(3,n)
in Fortra-3.1.1 Requirements
++-3.1.1 Requirements
- @@ -1163,8 +1163,8 @@ the leading dimension:
context
is notQMCKL_NULL_CONTEXT
[n][3]
in C and(3,n)
in Fortra-3.1.2 C header
++3.1.2 C header
-qmckl_exit_code qmckl_distance_rescaled ( @@ -1185,8 +1185,8 @@ the leading dimension:[n][3]
in C and(3,n)
in Fortra-3.1.3 Source
++3.1.3 Source
-integer function qmckl_distance_rescaled_f(context, transa, transb, m, n, & @@ -1356,8 +1356,8 @@ the leading dimension:[n][3]
in C and(3,n)
in Fortra--3.1.4 Performance
++3.1.4 Performance
This function is more efficient when
A
andB
are transposed. @@ -1366,12 +1366,12 @@ This function is more efficient whenA
andB
are trans-4 Rescaled Distance Derivatives
++4 Rescaled Distance Derivatives
--4.1
+qmckl_distance_rescaled_deriv_e
+4.1
qmckl_distance_rescaled_deriv_e
-
qmckl_distance_rescaled_deriv_e
computes the matrix of the gradient and laplacian of the @@ -1438,7 +1438,7 @@ If the input array is normal ('N'
), the xyz coordinates are in the leading dimension:[n][3]
in C and(3,n)
in Fortran.+
-1.1 Data structure
++1.1 Data structure
-typedef struct qmckl_electron_struct { @@ -707,8 +707,8 @@ this mechanism.-1.2 Access functions
++1.2 Access functions
-Access functions return
QMCKL_SUCCESS
when the data has been @@ -720,12 +720,12 @@ contains the requested data. Otherwise, this variable is untouched.-1.2.1 Number of electrons
++-1.2.1 Number of electrons
-1.2.2 Number of walkers
++-1.2.2 Number of walkers
A walker is a set of electron coordinates that are arguments of @@ -734,12 +734,12 @@ the wave function.
walk_num
is the number of walkers.-1.2.3 Scaling factors Kappa
++-1.2.3 Scaling factors Kappa
-1.2.4 Electron coordinates
++-1.2.4 Electron coordinates
Returns the current electron coordinates. The pointer is assumed @@ -789,8 +789,8 @@ returning the current points.
-1.3 Initialization functions
++-1.3 Initialization functions
To set the data relative to the electrons in the context, the @@ -884,8 +884,8 @@ in the context.
-1.4 Test
++1.4 Test
-/* Reference input data */ @@ -992,8 +992,8 @@ rc = qmckl_get_electron_coord (context, 'N'-2 Computation
++2 Computation
-The computed data is stored in the context so that it can be reused @@ -1006,12 +1006,12 @@ 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* const distance); @@ -1020,10 +1020,10 @@ current date is stored.-2.1.2 Compute
++2.1.2 Compute
-+
@@ -1128,8 +1128,8 @@ current date is stored. - -2.1.3 Test
++2.1.3 Test
-assert(qmckl_electron_provided(context)); @@ -1163,8 +1163,8 @@ rc = qmckl_get_electron_ee_distance(context, ee_distance);-2.2 Electron-electron rescaled distances
++2.2 Electron-electron rescaled distances
-
ee_distance_rescaled
stores the matrix of the rescaled distances between all @@ -1182,8 +1182,8 @@ where \(C_{ij}\) is the matrix of electron-electron distances.-2.2.1 Get
++2.2.1 Get
-qmckl_exit_code qmckl_get_electron_ee_distance_rescaled(qmckl_context context, double* const distance_rescaled); @@ -1192,10 +1192,10 @@ where \(C_{ij}\) is the matrix of electron-electron distances.-2.2.2 Compute
++2.2.2 Compute
-+
@@ -1308,8 +1308,8 @@ where \(C_{ij}\) is the matrix of electron-electron distances. - -