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add dim type for dimensioning variables in the trex.json

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q-posev 2021-09-22 10:56:25 +02:00
parent 389d265f7f
commit 0167a53d50
2 changed files with 80 additions and 71 deletions
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7
tools/generator_tools.py
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@ -132,7 +132,7 @@ def recursive_populate_file(fname: str, paths: dict, detailed_source: dict) -> N
# special case to uncomment check for positive dimensioning variables in templates # special case to uncomment check for positive dimensioning variables in templates
elif 'uncommented by the generator for dimensioning' in line: elif 'uncommented by the generator for dimensioning' in line:
# only uncomment and write the line if `num` is in the name # only uncomment and write the line if `num` is in the name
if 'num' in item: if 'dim' in detailed_source[item]['trex_json_int_type']:
templine = line.replace('//', '') templine = line.replace('//', '')
f_out.write(templine) f_out.write(templine)
# general case of recursive replacement of inline triggers # general case of recursive replacement of inline triggers
@ -478,7 +478,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
tmp_dict['group_num'] = tmp_num tmp_dict['group_num'] = tmp_num
num_dict[tmp_num] = tmp_dict num_dict[tmp_num] = tmp_dict
# TODO the line below is the same as for group_dset and can be exported from somewhere # TODO the arguments below are almost the same as for group_dset (except for trex_json_int_type) and can be exported from somewhere
if v2[0] == 'float': if v2[0] == 'float':
tmp_dict['datatype'] = 'double' tmp_dict['datatype'] = 'double'
tmp_dict['group_num_h5_dtype'] = 'native_double' tmp_dict['group_num_h5_dtype'] = 'native_double'
@ -492,7 +492,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
tmp_dict['group_num_std_dtype_out'] = '24.16e' tmp_dict['group_num_std_dtype_out'] = '24.16e'
tmp_dict['group_num_std_dtype_in'] = 'lf' tmp_dict['group_num_std_dtype_in'] = 'lf'
tmp_dict['group_num_py_dtype'] = 'float' tmp_dict['group_num_py_dtype'] = 'float'
elif v2[0] in ['int']: elif v2[0] in ['int', 'dim']:
tmp_dict['datatype'] = 'int64_t' tmp_dict['datatype'] = 'int64_t'
tmp_dict['group_num_h5_dtype'] = 'native_int64' tmp_dict['group_num_h5_dtype'] = 'native_int64'
tmp_dict['group_num_f_dtype_default']= 'integer(4)' tmp_dict['group_num_f_dtype_default']= 'integer(4)'
@ -505,6 +505,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
tmp_dict['group_num_std_dtype_out'] = '" PRId64 "' tmp_dict['group_num_std_dtype_out'] = '" PRId64 "'
tmp_dict['group_num_std_dtype_in'] = '" SCNd64 "' tmp_dict['group_num_std_dtype_in'] = '" SCNd64 "'
tmp_dict['group_num_py_dtype'] = 'int' tmp_dict['group_num_py_dtype'] = 'int'
tmp_dict['trex_json_int_type'] = v2[0]
return num_dict return num_dict

144
trex.org
View File

@ -16,6 +16,14 @@ column-major order (as in Fortran), and the ordering of the dimensions
is reversed in the produced ~trex.json~ configuration file as the library is is reversed in the produced ~trex.json~ configuration file as the library is
written in C. written in C.
TREXIO currently supports ~int~, ~float~ and ~str~ types for both single attributes and arrays.
Note, that some attributes might have ~dim~ type (e.g. ~num~ of the ~nucleus~ group).
This type is treated exactly the same as ~int~ with the only difference that ~dim~ variables
cannot be negative or zero. This additional constraint is required because ~dim~ attributes
are used internally to allocate memory and to check array boundaries in the memory-safe API.
Most of the times, the ~dim~ variables contain ~num~ suffix.
In Fortran, the arrays are 1-based and in most other languages the In Fortran, the arrays are 1-based and in most other languages the
arrays are 0-based. Hence, we introduce the ~index~ type which is an arrays are 0-based. Hence, we introduce the ~index~ type which is an
1-based ~int~ in the Fortran interface and 0-based otherwise. 1-based ~int~ in the Fortran interface and 0-based otherwise.
@ -35,9 +43,9 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+NAME: metadata #+NAME: metadata
| Variable | Type | Dimensions (for arrays) | Description | | Variable | Type | Dimensions (for arrays) | Description |
|-------------------+-------+-------------------------+------------------------------------------| |-------------------+-------+-------------------------+------------------------------------------|
| ~code_num~ | ~int~ | | Number of codes used to produce the file | | ~code_num~ | ~dim~ | | Number of codes used to produce the file |
| ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used | | ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used |
| ~author_num~ | ~int~ | | Number of authors of the file | | ~author_num~ | ~dim~ | | Number of authors of the file |
| ~author~ | ~str~ | ~(metadata.author_num)~ | Names of the authors of the file | | ~author~ | ~str~ | ~(metadata.author_num)~ | Names of the authors of the file |
| ~package_version~ | ~str~ | | TREXIO version used to produce the file | | ~package_version~ | ~str~ | | TREXIO version used to produce the file |
| ~description~ | ~str~ | | Text describing the content of file | | ~description~ | ~str~ | | Text describing the content of file |
@ -47,9 +55,9 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
:RESULTS: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"metadata": { "metadata": {
"code_num" : [ "int", [] ] "code_num" : [ "dim", [] ]
, "code" : [ "str", [ "metadata.code_num" ] ] , "code" : [ "str", [ "metadata.code_num" ] ]
, "author_num" : [ "int", [] ] , "author_num" : [ "dim", [] ]
, "author" : [ "str", [ "metadata.author_num" ] ] , "author" : [ "str", [ "metadata.author_num" ] ]
, "package_version" : [ "str", [] ] , "package_version" : [ "str", [] ]
, "description" : [ "str", [] ] , "description" : [ "str", [] ]
@ -65,19 +73,19 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+NAME:electron #+NAME:electron
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|----------+-------+------------+-------------------------------------| |----------+-------+------------+-------------------------------------|
| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons | | ~up_num~ | ~dim~ | | Number of \uparrow-spin electrons |
| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons | | ~dn_num~ | ~dim~ | | Number of \downarrow-spin electrons |
#+CALL: json(data=electron, title="electron") #+CALL: json(data=electron, title="electron")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"electron": { "electron": {
"up_num" : [ "int", [] ] "up_num" : [ "dim", [] ]
, "dn_num" : [ "int", [] ] , "dn_num" : [ "dim", [] ]
} , } ,
#+end_src #+end_src
:end: :END:
* Nucleus (nucleus group) * Nucleus (nucleus group)
@ -87,7 +95,7 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+NAME: nucleus #+NAME: nucleus
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------+---------+-------------------+--------------------------| |---------------+---------+-------------------+--------------------------|
| ~num~ | ~int~ | | Number of nuclei | | ~num~ | ~dim~ | | Number of nuclei |
| ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei | | ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei |
| ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms | | ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms |
| ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels | | ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels |
@ -95,17 +103,17 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+CALL: json(data=nucleus, title="nucleus") #+CALL: json(data=nucleus, title="nucleus")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"nucleus": { "nucleus": {
"num" : [ "int" , [] ] "num" : [ "dim" , [] ]
, "charge" : [ "float", [ "nucleus.num" ] ] , "charge" : [ "float", [ "nucleus.num" ] ]
, "coord" : [ "float", [ "nucleus.num", "3" ] ] , "coord" : [ "float", [ "nucleus.num", "3" ] ]
, "label" : [ "str" , [ "nucleus.num" ] ] , "label" : [ "str" , [ "nucleus.num" ] ]
, "point_group" : [ "str" , [] ] , "point_group" : [ "str" , [] ]
} , } ,
#+end_src #+end_src
:end: :END:
* Effective core potentials (ecp group) * Effective core potentials (ecp group)
@ -135,12 +143,12 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
| ~lmax_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max} + 1$, one higher than the maximum angular momentum in the removed core orbitals | | ~lmax_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max} + 1$, one higher than the maximum angular momentum in the removed core orbitals |
| ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove | | ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove |
| ~local_n~ | ~int~ | ~(nucleus.num)~ | Number of local functions $N_{q \ell}$ | | ~local_n~ | ~int~ | ~(nucleus.num)~ | Number of local functions $N_{q \ell}$ |
| ~local_num_n_max~ | ~int~ | | Maximum value of ~local_n~, used for dimensioning arrays | | ~local_num_n_max~ | ~dim~ | | Maximum value of ~local_n~, used for dimensioning arrays |
| ~local_exponent~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell_{\max}}$ | | ~local_exponent~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell_{\max}}$ |
| ~local_coef~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\beta_{A q \ell_{\max}}$ | | ~local_coef~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\beta_{A q \ell_{\max}}$ |
| ~local_power~ | ~int~ | ~(ecp.local_num_n_max, nucleus.num)~ | $n_{A q \ell_{\max}}$ | | ~local_power~ | ~int~ | ~(ecp.local_num_n_max, nucleus.num)~ | $n_{A q \ell_{\max}}$ |
| ~non_local_n~ | ~int~ | ~(nucleus.num)~ | $N_{q \ell_{\max}}$ | | ~non_local_n~ | ~int~ | ~(nucleus.num)~ | $N_{q \ell_{\max}}$ |
| ~non_local_num_n_max~ | ~int~ | | Maximum value of ~non_local_n~, used for dimensioning arrays | | ~non_local_num_n_max~ | ~dim~ | | Maximum value of ~non_local_n~, used for dimensioning arrays |
| ~non_local_exponent~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell}$ | | ~non_local_exponent~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell}$ |
| ~non_local_coef~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\beta_{A q \ell}$ | | ~non_local_coef~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\beta_{A q \ell}$ |
| ~non_local_power~ | ~int~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $n_{A q \ell}$ | | ~non_local_power~ | ~int~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $n_{A q \ell}$ |
@ -148,24 +156,24 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+CALL: json(data=ecp, title="ecp") #+CALL: json(data=ecp, title="ecp")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"ecp": { "ecp": {
"lmax_plus_1" : [ "int" , [ "nucleus.num" ] ] "lmax_plus_1" : [ "int" , [ "nucleus.num" ] ]
, "z_core" : [ "float", [ "nucleus.num" ] ] , "z_core" : [ "float", [ "nucleus.num" ] ]
, "local_n" : [ "int" , [ "nucleus.num" ] ] , "local_n" : [ "int" , [ "nucleus.num" ] ]
, "local_num_n_max" : [ "int" , [] ] , "local_num_n_max" : [ "dim" , [] ]
, "local_exponent" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ] , "local_exponent" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
, "local_coef" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ] , "local_coef" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
, "local_power" : [ "int" , [ "nucleus.num", "ecp.local_num_n_max" ] ] , "local_power" : [ "int" , [ "nucleus.num", "ecp.local_num_n_max" ] ]
, "non_local_n" : [ "int" , [ "nucleus.num" ] ] , "non_local_n" : [ "int" , [ "nucleus.num" ] ]
, "non_local_num_n_max" : [ "int" , [] ] , "non_local_num_n_max" : [ "dim" , [] ]
, "non_local_exponent" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ] , "non_local_exponent" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
, "non_local_coef" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ] , "non_local_coef" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
, "non_local_power" : [ "int" , [ "nucleus.num", "ecp.non_local_num_n_max" ] ] , "non_local_power" : [ "int" , [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
} , } ,
#+end_src #+end_src
:end: :END:
* Basis set (basis group) * Basis set (basis group)
@ -210,8 +218,8 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------------+---------+--------------------+----------------------------------------------------------| |---------------------+---------+--------------------+----------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" | | ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
| ~num~ | ~int~ | | Total Number of shells | | ~num~ | ~dim~ | | Total Number of shells |
| ~prim_num~ | ~int~ | | Total number of primitives | | ~prim_num~ | ~dim~ | | Total number of primitives |
| ~nucleus_index~ | ~index~ | ~(nucleus.num)~ | Index of the first shell of each nucleus ($A$) | | ~nucleus_index~ | ~index~ | ~(nucleus.num)~ | Index of the first shell of each nucleus ($A$) |
| ~nucleus_shell_num~ | ~int~ | ~(nucleus.num)~ | Number of shells for each nucleus | | ~nucleus_shell_num~ | ~int~ | ~(nucleus.num)~ | Number of shells for each nucleus |
| ~shell_ang_mom~ | ~int~ | ~(basis.num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ | | ~shell_ang_mom~ | ~int~ | ~(basis.num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ |
@ -225,24 +233,24 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+CALL: json(data=basis, title="basis") #+CALL: json(data=basis, title="basis")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"basis": { "basis": {
"type" : [ "str" , [] ] "type" : [ "str" , [] ]
, "num" : [ "int" , [] ] , "num" : [ "dim" , [] ]
, "prim_num" : [ "int" , [] ] , "prim_num" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "nucleus.num" ] ] , "nucleus_index" : [ "index", [ "nucleus.num" ] ]
, "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ] , "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ]
, "shell_ang_mom" : [ "int" , [ "basis.num" ] ] , "shell_ang_mom" : [ "int" , [ "basis.num" ] ]
, "shell_prim_num" : [ "int" , [ "basis.num" ] ] , "shell_prim_num" : [ "int" , [ "basis.num" ] ]
, "shell_factor" : [ "float", [ "basis.num" ] ] , "shell_factor" : [ "float", [ "basis.num" ] ]
, "shell_prim_index" : [ "index", [ "basis.num" ] ] , "shell_prim_index" : [ "index", [ "basis.num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ] , "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ] , "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ] , "prim_factor" : [ "float", [ "basis.prim_num" ] ]
} , } ,
#+end_src #+end_src
:end: :END:
For example, consider H_2 with the following basis set (in GAMESS For example, consider H_2 with the following basis set (in GAMESS
format), where both the AOs and primitives are considered normalized: format), where both the AOs and primitives are considered normalized:
@ -348,23 +356,23 @@ prim_factor =
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|-----------------+---------+------------+---------------------------------| |-----------------+---------+------------+---------------------------------|
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false | | ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
| ~num~ | ~int~ | | Total number of atomic orbitals | | ~num~ | ~dim~ | | Total number of atomic orbitals |
| ~shell~ | ~index~ | ~(ao.num)~ | basis set shell for each AO | | ~shell~ | ~index~ | ~(ao.num)~ | basis set shell for each AO |
| ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factors | | ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factors |
#+CALL: json(data=ao, title="ao") #+CALL: json(data=ao, title="ao")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"ao": { "ao": {
"cartesian" : [ "int" , [] ] "cartesian" : [ "int" , [] ]
, "num" : [ "int" , [] ] , "num" : [ "dim" , [] ]
, "shell" : [ "index", [ "ao.num" ] ] , "shell" : [ "index", [ "ao.num" ] ]
, "normalization" : [ "float", [ "ao.num" ] ] , "normalization" : [ "float", [ "ao.num" ] ]
} , } ,
#+end_src #+end_src
:end: :END:
** One-electron integrals (~ao_1e_int~ group) ** One-electron integrals (~ao_1e_int~ group)
:PROPERTIES: :PROPERTIES:
@ -453,7 +461,7 @@ prim_factor =
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------+---------+--------------------+--------------------------------------------------------------------------| |---------------+---------+--------------------+--------------------------------------------------------------------------|
| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) | | ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
| ~num~ | ~int~ | | Number of MOs | | ~num~ | ~dim~ | | Number of MOs |
| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients | | ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted | | ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group | | ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
@ -462,18 +470,18 @@ prim_factor =
#+CALL: json(data=mo, title="mo") #+CALL: json(data=mo, title="mo")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"mo": { "mo": {
"type" : [ "str" , [] ] "type" : [ "str" , [] ]
, "num" : [ "int" , [] ] , "num" : [ "dim" , [] ]
, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ] , "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
, "class" : [ "str" , [ "mo.num" ] ] , "class" : [ "str" , [ "mo.num" ] ]
, "symmetry" : [ "str" , [ "mo.num" ] ] , "symmetry" : [ "str" , [ "mo.num" ] ]
, "occupation" : [ "float", [ "mo.num" ] ] , "occupation" : [ "float", [ "mo.num" ] ]
} , } ,
#+end_src #+end_src
:end: :END:
** One-electron integrals (~mo_1e_int~ group) ** One-electron integrals (~mo_1e_int~ group)