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https://github.com/TREX-CoE/trexio.git
synced 2024-12-31 08:36:08 +01:00
add dim type for dimensioning variables in the trex.json
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parent
389d265f7f
commit
0167a53d50
@ -132,7 +132,7 @@ def recursive_populate_file(fname: str, paths: dict, detailed_source: dict) -> N
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# special case to uncomment check for positive dimensioning variables in templates
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elif 'uncommented by the generator for dimensioning' in line:
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# only uncomment and write the line if `num` is in the name
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if 'num' in item:
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if 'dim' in detailed_source[item]['trex_json_int_type']:
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templine = line.replace('//', '')
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f_out.write(templine)
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# general case of recursive replacement of inline triggers
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@ -478,7 +478,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
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tmp_dict['group_num'] = tmp_num
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num_dict[tmp_num] = tmp_dict
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# TODO the line below is the same as for group_dset and can be exported from somewhere
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# TODO the arguments below are almost the same as for group_dset (except for trex_json_int_type) and can be exported from somewhere
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if v2[0] == 'float':
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tmp_dict['datatype'] = 'double'
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tmp_dict['group_num_h5_dtype'] = 'native_double'
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@ -492,7 +492,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
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tmp_dict['group_num_std_dtype_out'] = '24.16e'
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tmp_dict['group_num_std_dtype_in'] = 'lf'
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tmp_dict['group_num_py_dtype'] = 'float'
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elif v2[0] in ['int']:
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elif v2[0] in ['int', 'dim']:
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tmp_dict['datatype'] = 'int64_t'
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tmp_dict['group_num_h5_dtype'] = 'native_int64'
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tmp_dict['group_num_f_dtype_default']= 'integer(4)'
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@ -505,6 +505,7 @@ def get_detailed_num_dict (configuration: dict) -> dict:
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tmp_dict['group_num_std_dtype_out'] = '" PRId64 "'
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tmp_dict['group_num_std_dtype_in'] = '" SCNd64 "'
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tmp_dict['group_num_py_dtype'] = 'int'
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tmp_dict['trex_json_int_type'] = v2[0]
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return num_dict
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144
trex.org
144
trex.org
@ -16,6 +16,14 @@ column-major order (as in Fortran), and the ordering of the dimensions
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is reversed in the produced ~trex.json~ configuration file as the library is
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written in C.
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TREXIO currently supports ~int~, ~float~ and ~str~ types for both single attributes and arrays.
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Note, that some attributes might have ~dim~ type (e.g. ~num~ of the ~nucleus~ group).
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This type is treated exactly the same as ~int~ with the only difference that ~dim~ variables
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cannot be negative or zero. This additional constraint is required because ~dim~ attributes
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are used internally to allocate memory and to check array boundaries in the memory-safe API.
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Most of the times, the ~dim~ variables contain ~num~ suffix.
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In Fortran, the arrays are 1-based and in most other languages the
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arrays are 0-based. Hence, we introduce the ~index~ type which is an
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1-based ~int~ in the Fortran interface and 0-based otherwise.
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@ -35,9 +43,9 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+NAME: metadata
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| Variable | Type | Dimensions (for arrays) | Description |
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|-------------------+-------+-------------------------+------------------------------------------|
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| ~code_num~ | ~int~ | | Number of codes used to produce the file |
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| ~code_num~ | ~dim~ | | Number of codes used to produce the file |
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| ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used |
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| ~author_num~ | ~int~ | | Number of authors of the file |
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| ~author_num~ | ~dim~ | | Number of authors of the file |
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| ~author~ | ~str~ | ~(metadata.author_num)~ | Names of the authors of the file |
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| ~package_version~ | ~str~ | | TREXIO version used to produce the file |
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| ~description~ | ~str~ | | Text describing the content of file |
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@ -47,9 +55,9 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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:RESULTS:
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#+begin_src python :tangle trex.json
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"metadata": {
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"code_num" : [ "int", [] ]
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"code_num" : [ "dim", [] ]
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, "code" : [ "str", [ "metadata.code_num" ] ]
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, "author_num" : [ "int", [] ]
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, "author_num" : [ "dim", [] ]
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, "author" : [ "str", [ "metadata.author_num" ] ]
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, "package_version" : [ "str", [] ]
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, "description" : [ "str", [] ]
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@ -65,19 +73,19 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+NAME:electron
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| Variable | Type | Dimensions | Description |
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|----------+-------+------------+-------------------------------------|
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| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons |
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| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons |
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| ~up_num~ | ~dim~ | | Number of \uparrow-spin electrons |
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| ~dn_num~ | ~dim~ | | Number of \downarrow-spin electrons |
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#+CALL: json(data=electron, title="electron")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"electron": {
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"up_num" : [ "int", [] ]
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, "dn_num" : [ "int", [] ]
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"up_num" : [ "dim", [] ]
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, "dn_num" : [ "dim", [] ]
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} ,
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#+end_src
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:end:
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:END:
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* Nucleus (nucleus group)
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@ -87,7 +95,7 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+NAME: nucleus
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| Variable | Type | Dimensions | Description |
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|---------------+---------+-------------------+--------------------------|
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| ~num~ | ~int~ | | Number of nuclei |
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| ~num~ | ~dim~ | | Number of nuclei |
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| ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei |
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| ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms |
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| ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels |
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@ -95,17 +103,17 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+CALL: json(data=nucleus, title="nucleus")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"nucleus": {
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"num" : [ "int" , [] ]
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, "charge" : [ "float", [ "nucleus.num" ] ]
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, "coord" : [ "float", [ "nucleus.num", "3" ] ]
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, "label" : [ "str" , [ "nucleus.num" ] ]
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, "point_group" : [ "str" , [] ]
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"num" : [ "dim" , [] ]
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, "charge" : [ "float", [ "nucleus.num" ] ]
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, "coord" : [ "float", [ "nucleus.num", "3" ] ]
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, "label" : [ "str" , [ "nucleus.num" ] ]
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, "point_group" : [ "str" , [] ]
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} ,
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#+end_src
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:end:
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:END:
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* Effective core potentials (ecp group)
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@ -135,12 +143,12 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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| ~lmax_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max} + 1$, one higher than the maximum angular momentum in the removed core orbitals |
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| ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove |
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| ~local_n~ | ~int~ | ~(nucleus.num)~ | Number of local functions $N_{q \ell}$ |
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| ~local_num_n_max~ | ~int~ | | Maximum value of ~local_n~, used for dimensioning arrays |
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| ~local_exponent~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell_{\max}}$ |
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| ~local_coef~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\beta_{A q \ell_{\max}}$ |
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| ~local_num_n_max~ | ~dim~ | | Maximum value of ~local_n~, used for dimensioning arrays |
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| ~local_exponent~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell_{\max}}$ |
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| ~local_coef~ | ~float~ | ~(ecp.local_num_n_max, nucleus.num)~ | $\beta_{A q \ell_{\max}}$ |
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| ~local_power~ | ~int~ | ~(ecp.local_num_n_max, nucleus.num)~ | $n_{A q \ell_{\max}}$ |
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| ~non_local_n~ | ~int~ | ~(nucleus.num)~ | $N_{q \ell_{\max}}$ |
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| ~non_local_num_n_max~ | ~int~ | | Maximum value of ~non_local_n~, used for dimensioning arrays |
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| ~non_local_num_n_max~ | ~dim~ | | Maximum value of ~non_local_n~, used for dimensioning arrays |
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| ~non_local_exponent~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\alpha_{A q \ell}$ |
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| ~non_local_coef~ | ~float~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $\beta_{A q \ell}$ |
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| ~non_local_power~ | ~int~ | ~(ecp.non_local_num_n_max, nucleus.num)~ | $n_{A q \ell}$ |
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@ -148,24 +156,24 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+CALL: json(data=ecp, title="ecp")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"ecp": {
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"lmax_plus_1" : [ "int" , [ "nucleus.num" ] ]
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, "z_core" : [ "float", [ "nucleus.num" ] ]
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, "local_n" : [ "int" , [ "nucleus.num" ] ]
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, "local_num_n_max" : [ "int" , [] ]
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, "local_exponent" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "local_coef" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "local_power" : [ "int" , [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "non_local_n" : [ "int" , [ "nucleus.num" ] ]
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, "non_local_num_n_max" : [ "int" , [] ]
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, "non_local_exponent" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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, "non_local_coef" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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, "non_local_power" : [ "int" , [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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"lmax_plus_1" : [ "int" , [ "nucleus.num" ] ]
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, "z_core" : [ "float", [ "nucleus.num" ] ]
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, "local_n" : [ "int" , [ "nucleus.num" ] ]
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, "local_num_n_max" : [ "dim" , [] ]
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, "local_exponent" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "local_coef" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "local_power" : [ "int" , [ "nucleus.num", "ecp.local_num_n_max" ] ]
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, "non_local_n" : [ "int" , [ "nucleus.num" ] ]
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, "non_local_num_n_max" : [ "dim" , [] ]
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, "non_local_exponent" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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, "non_local_coef" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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, "non_local_power" : [ "int" , [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
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} ,
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#+end_src
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:end:
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:END:
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* Basis set (basis group)
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@ -210,8 +218,8 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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| Variable | Type | Dimensions | Description |
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|---------------------+---------+--------------------+----------------------------------------------------------|
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| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
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| ~num~ | ~int~ | | Total Number of shells |
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| ~prim_num~ | ~int~ | | Total number of primitives |
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| ~num~ | ~dim~ | | Total Number of shells |
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| ~prim_num~ | ~dim~ | | Total number of primitives |
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| ~nucleus_index~ | ~index~ | ~(nucleus.num)~ | Index of the first shell of each nucleus ($A$) |
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| ~nucleus_shell_num~ | ~int~ | ~(nucleus.num)~ | Number of shells for each nucleus |
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| ~shell_ang_mom~ | ~int~ | ~(basis.num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ |
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@ -225,24 +233,24 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+CALL: json(data=basis, title="basis")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"basis": {
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"type" : [ "str" , [] ]
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, "num" : [ "int" , [] ]
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, "prim_num" : [ "int" , [] ]
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, "nucleus_index" : [ "index", [ "nucleus.num" ] ]
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, "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.num" ] ]
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, "shell_prim_num" : [ "int" , [ "basis.num" ] ]
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, "shell_factor" : [ "float", [ "basis.num" ] ]
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, "shell_prim_index" : [ "index", [ "basis.num" ] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
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"type" : [ "str" , [] ]
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, "num" : [ "dim" , [] ]
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, "prim_num" : [ "dim" , [] ]
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, "nucleus_index" : [ "index", [ "nucleus.num" ] ]
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, "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.num" ] ]
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, "shell_prim_num" : [ "int" , [ "basis.num" ] ]
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, "shell_factor" : [ "float", [ "basis.num" ] ]
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, "shell_prim_index" : [ "index", [ "basis.num" ] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
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} ,
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#+end_src
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:end:
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:END:
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For example, consider H_2 with the following basis set (in GAMESS
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format), where both the AOs and primitives are considered normalized:
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@ -348,23 +356,23 @@ prim_factor =
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| Variable | Type | Dimensions | Description |
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|-----------------+---------+------------+---------------------------------|
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| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
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| ~num~ | ~int~ | | Total number of atomic orbitals |
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| ~num~ | ~dim~ | | Total number of atomic orbitals |
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| ~shell~ | ~index~ | ~(ao.num)~ | basis set shell for each AO |
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| ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factors |
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#+CALL: json(data=ao, title="ao")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"ao": {
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"cartesian" : [ "int" , [] ]
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, "num" : [ "int" , [] ]
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, "shell" : [ "index", [ "ao.num" ] ]
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, "normalization" : [ "float", [ "ao.num" ] ]
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"cartesian" : [ "int" , [] ]
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, "num" : [ "dim" , [] ]
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, "shell" : [ "index", [ "ao.num" ] ]
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, "normalization" : [ "float", [ "ao.num" ] ]
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} ,
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#+end_src
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:end:
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:END:
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** One-electron integrals (~ao_1e_int~ group)
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:PROPERTIES:
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@ -453,7 +461,7 @@ prim_factor =
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| Variable | Type | Dimensions | Description |
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|---------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
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| ~num~ | ~int~ | | Number of MOs |
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| ~num~ | ~dim~ | | Number of MOs |
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| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
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| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
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| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
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@ -462,18 +470,18 @@ prim_factor =
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#+CALL: json(data=mo, title="mo")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"mo": {
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"type" : [ "str" , [] ]
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, "num" : [ "int" , [] ]
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, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
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, "class" : [ "str" , [ "mo.num" ] ]
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, "symmetry" : [ "str" , [ "mo.num" ] ]
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, "occupation" : [ "float", [ "mo.num" ] ]
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"type" : [ "str" , [] ]
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, "num" : [ "dim" , [] ]
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, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
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, "class" : [ "str" , [ "mo.num" ] ]
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, "symmetry" : [ "str" , [ "mo.num" ] ]
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, "occupation" : [ "float", [ "mo.num" ] ]
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} ,
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#+end_src
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:end:
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:END:
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** One-electron integrals (~mo_1e_int~ group)
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