mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-12-22 12:23:54 +01:00
Added trex.org to generate json
This commit is contained in:
parent
1d5c452071
commit
9ec75c2892
@ -12,6 +12,21 @@ TREXIO_ROOT=$(dirname "${PWD}../")
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readonly SRC=${TREXIO_ROOT}/src
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readonly TOOLS=${TREXIO_ROOT}/tools
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# Function to produce TREXIO source files from org-mode files
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function tangle()
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{
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local command="(org-babel-tangle-file \"$1\")"
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emacs --batch \
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--eval "(require 'org)" \
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--eval "(org-babel-do-load-languages 'org-babel-load-languages '((python . t)))" \
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--eval "(setq org-confirm-babel-evaluate nil)" \
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--eval "$command"
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}
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# Create trex.json file
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cd ${TREXIO_ROOT}
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tangle trex.org
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# Go to src directory
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cd ${SRC}
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@ -38,17 +53,6 @@ rm -f -- templates_front/populated/*
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rm -f -- templates_text/populated/*
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rm -f -- templates_hdf5/populated/*
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# Function to produce TREXIO source files from org-mode files
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function tangle()
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{
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local command="(org-babel-tangle-file \"$1\")"
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emacs --batch \
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--eval "(require 'org)" \
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--eval "(org-babel-do-load-languages 'org-babel-load-languages '((python . t)))" \
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--eval "(setq org-confirm-babel-evaluate nil)" \
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--eval "$command"
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}
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# Produce source files for front end
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echo "tangle org files to generate templates"
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cd templates_front
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176
trex.json
176
trex.json
@ -1,99 +1,103 @@
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{
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"metadata": {
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"code_num" : [ "int" , [ ] ]
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, "code" : [ "char", [ "metadata.code_num" , "128" ] ]
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, "author_num" : [ "int" , [ ] ]
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, "author" : [ "char", [ "metadata.author_num", "128" ] ]
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, "description_length" : [ "int" , [ ] ]
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, "description" : [ "char", [ "metadata.description_length" ] ]
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},
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"electron": {
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"up_num" : [ "int", [] ]
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, "dn_num" : [ "int", [] ]
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},
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"metadata": {
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"code_num" : [ "int", [] ]
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, "code " : [ "str", [ "metadata.code_num" ] ]
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, "author_num" : [ "int", [] ]
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, "author" : [ "str", [ "metadata.author_num" ] ]
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, "description" : [ "str", [] ]
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} ,
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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" : [ "char" , [ "nucleus.num", "32" ] ]
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, "point_group" : [ "char" , [ "32" ] ]
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},
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"electron": {
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"up_num" : [ "int", [] ]
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, "dn_num" : [ "int", [] ]
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} ,
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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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},
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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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} ,
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"basis" : {
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"type" : [ "char" , [ "32" ] ]
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, "shell_num" : [ "int" , [ ] ]
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, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
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, "shell_center" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_prim_num" : [ "int" , [ "basis.shell_num" ] ]
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, "prim_index" : [ "int" , [ "basis.shell_num" ] ]
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, "prim_num" : [ "int" , [ ] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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},
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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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} ,
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"ao" : {
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"num" : [ "int" , [ ] ]
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, "cartesian" : [ "int" , [ ] ]
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, "shell" : [ "int" , [ "ao.num" ] ]
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, "normalization" : [ "float", [ "ao.num" ] ]
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},
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"basis": {
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"type" : [ "str" , [] ]
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, "shell_num" : [ "int" , [] ]
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, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
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, "shell_center" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_prim_num" : [ "int" , [ "basis.shell_num" ] ]
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, "prim_index" : [ "int" , [ "basis.shell_num" ] ]
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, "prim_num" : [ "int" , [] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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} ,
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"ao_1e_int" : {
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"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
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, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
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, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp_local" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp_non_local" : [ "float", [ "ao.num", "ao.num" ] ]
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, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
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},
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"ao": {
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"num" : [ "int" , [] ]
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, "cartesian" : [ "int" , [] ]
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, "shell" : [ "int" , [] ]
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, "normalization" : [ "float", [] ]
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} ,
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"ao_2e_int" : {
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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},
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"ao_1e_int": {
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"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
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, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
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, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp_local" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp_non_local" : [ "float", [ "ao.num", "ao.num" ] ]
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, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
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} ,
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"mo" : {
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"type" : [ "char" , [ "32" ] ]
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, "num" : [ "int" , [ ] ]
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, "coef" : [ "float", [ "ao.num", "mo.num" ] ]
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, "class" : [ "char" , [ "mo.num", "32" ] ]
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, "symmetry" : [ "char" , [ "mo.num", "32" ] ]
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, "occupation" : [ "float", [ "mo.num" ] ]
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},
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"ao_2e_int": {
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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} ,
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"mo_1e_int" : {
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"kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
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, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp_local" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp_non_local" : [ "float", [ "mo.num", "mo.num" ] ]
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, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
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},
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"mo": {
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"type" : [ "str" , [] ]
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, "num" : [ "int" , [] ]
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, "coef" : [ "float", [ "ao.num", "mo.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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"mo_2e_int" : {
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"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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},
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"mo_1e_int": {
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"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
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, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
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, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp_local" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp_non_local" : [ "float", [ "mo.num", "mo.num" ] ]
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, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
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} ,
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"mo_2e_int": {
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"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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} ,
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"rdm": {
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"one_e" : [ "float" , [ "mo.num", "mo.num" ] ]
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, "one_e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
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, "one_e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
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, "two_e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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}
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"rdm" : {
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"one_e" : [ "float", [ "mo.num", "mo.num" ] ]
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, "one_e_up" : [ "float", [ "mo.num", "mo.num" ] ]
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, "one_e_dn" : [ "float", [ "mo.num", "mo.num" ] ]
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, "two_e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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}
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}
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392
trex.org
Normal file
392
trex.org
Normal file
@ -0,0 +1,392 @@
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#+TITLE: TREX Configuration file
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All the quantities are saved in atomic units.
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#+begin_src python :tangle trex.json
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{
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#+end_src
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* Metadata
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#+NAME: metadata
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| ~code_num~ | ~int~ | | 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~ | ~str~ | ~(metadata.author_num)~ | Names of the authors of the file |
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| ~description~ | ~str~ | | Text describing the content of file |
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#+CALL: json(data=metadata, title="metadata")
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#+RESULTS:
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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 " : [ "str", [ "metadata.code_num" ] ]
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, "author_num" : [ "int", [] ]
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, "author" : [ "str", [ "metadata.author_num" ] ]
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, "description" : [ "str", [] ]
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} ,
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#+end_src
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:end:
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* Electron
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#+NAME:electron
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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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#+CALL: json(data=electron, title="electron")
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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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} ,
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#+end_src
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:end:
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* Nucleus
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#+NAME: nucleus
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| ~num~ | ~int~ | | Number of nuclei |
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| ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei |
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| ~coord~ | ~float~ | ~(nucleus.num, 3)~ | Coordinates of the atoms |
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| ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels |
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| ~point_group~ | ~str~ | | Symmetry point group |
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#+CALL: json(data=nucleus, title="nucleus")
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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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} ,
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#+end_src
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:end:
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* TODO Effective core potentials
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- $\hat{V}_\text{ecp,l} =$ : local component
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- $\hat{V}_\text{ecp,nl} =$ : non-local component
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#+NAME: ecp
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| ~lmax_plus_1~ | ~int~ | ~(nucleus.num)~ | $l_{\max} + 1$ |
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| ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove |
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| ~local_n~ | ~int~ | ~(nucleus.num)~ | Number of local function |
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| ~local_num_n_max~ | ~int~ | | Maximum value of ~local_n~ |
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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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#+CALL: json(data=ecp, title="ecp")
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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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} ,
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#+end_src
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:end:
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* Basis set
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#+NAME: basis
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| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
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| ~shell_num~ | ~int~ | | Total Number of shells |
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| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of the shell |
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| ~shell_center~ | ~int~ | ~(basis.shell_num)~ | Nucleus on which the shell is centered |
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| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ |
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| ~shell_prim_num~ | ~int~ | ~(basis.shell_num)~ | Number of primitives in the shell |
|
||||
| ~prim_index~ | ~int~ | ~(basis.shell_num)~ | Index of the first primitive in the complete list |
|
||||
| ~prim_num~ | ~int~ | | Total number of primitives |
|
||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives |
|
||||
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives |
|
||||
|
||||
#+CALL: json(data=basis, title="basis")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"basis": {
|
||||
"type" : [ "str" , [] ]
|
||||
, "shell_num" : [ "int" , [] ]
|
||||
, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
|
||||
, "shell_center" : [ "int" , [ "basis.shell_num" ] ]
|
||||
, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
|
||||
, "shell_prim_num" : [ "int" , [ "basis.shell_num" ] ]
|
||||
, "prim_index" : [ "int" , [ "basis.shell_num" ] ]
|
||||
, "prim_num" : [ "int" , [] ]
|
||||
, "exponent" : [ "float", [ "basis.prim_num" ] ]
|
||||
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Atomic orbitals
|
||||
|
||||
#+NAME: ao
|
||||
| ~num~ | ~int~ | | Number of atomic orbitals |
|
||||
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
|
||||
| ~shell~ | ~int~ | ~ao.num~ | ID of the basis set shell |
|
||||
| ~normalization~ | ~float~ | ~ao.num~ | Normalization factor of the AOs |
|
||||
|
||||
#+CALL: json(data=ao, title="ao")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"ao": {
|
||||
"num" : [ "int" , [] ]
|
||||
, "cartesian" : [ "int" , [] ]
|
||||
, "shell" : [ "int" , [] ]
|
||||
, "normalization" : [ "float", [] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** One-electron integrals
|
||||
|
||||
- \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
\sum_{i=1}^{N_\text{elec}} \frac{-Q_A }{\vert \mathbf{R}_A -
|
||||
\mathbf{r}_i \vert} \] : electron-nucleus attractive potential,
|
||||
- \[ \hat{T}_{\text{e}} =
|
||||
\sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy
|
||||
- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} +
|
||||
\hat{V}_\text{ecp,l} + \hat{V}_\text{ecp,nl}$ : core electronic Hamiltonian
|
||||
|
||||
The one-electron integrals for a one-electron operator $\hat{O}$ are
|
||||
\[ \langle p \vert \hat{O} \vert q \rangle \], returned as a matrix
|
||||
over atomic orbitals.
|
||||
|
||||
#+NAME: ao_1e_int
|
||||
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l} \vert q \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl} \vert q \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
||||
|
||||
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"ao_1e_int": {
|
||||
"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
, "ecp_local" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
, "ecp_non_local" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** Two-electron integrals
|
||||
|
||||
The two-electron integrals for a two-electron operator $\hat{O}$ are
|
||||
\[ \langle p q \vert \hat{O} \vert r s \rangle \] in physicists
|
||||
notation or \[ ( pr \vert \hat{O} \vert qs ) \] in chemists
|
||||
notation, where $p,q,r,s$ are indices over atomic orbitals.
|
||||
|
||||
Functions are provided to get the indices in physicists or chemists
|
||||
notation.
|
||||
|
||||
# TODO: Physicist / Chemist functions
|
||||
|
||||
- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
|
||||
- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}}
|
||||
\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
|
||||
|
||||
#+NAME: ao_2e_int
|
||||
| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
|
||||
| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals |
|
||||
|
||||
#+CALL: json(data=ao_2e_int, title="ao_2e_int")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"ao_2e_int": {
|
||||
"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
|
||||
, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Molecular orbitals
|
||||
|
||||
#+NAME: mo
|
||||
| ~type~ | ~str~ | | String identify the set of MOs |
|
||||
| ~num~ | ~int~ | | Number of MOs |
|
||||
| ~coef~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
|
||||
| ~class~ | ~str~ | ~(mo.num)~ | Core, Inactive, Active, Virtual, Deleted |
|
||||
| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
|
||||
| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
|
||||
|
||||
#+CALL: json(data=mo, title="mo")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"mo": {
|
||||
"type" : [ "str" , [] ]
|
||||
, "num" : [ "int" , [] ]
|
||||
, "coef" : [ "float", [ "ao.num", "mo.num" ] ]
|
||||
, "class" : [ "str" , [ "mo.num" ] ]
|
||||
, "symmetry" : [ "str" , [ "mo.num" ] ]
|
||||
, "occupation" : [ "float", [ "mo.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** One-electron integrals
|
||||
|
||||
The operators as the same as those defined in the AO one-electron
|
||||
integrals section. Here, the integrals are given in the basis of
|
||||
molecular orbitals.
|
||||
|
||||
#+NAME: mo_1e_int
|
||||
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l} \vert j \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl} \vert j \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
||||
|
||||
#+CALL: json(data=mo_1e_int, title="mo_1e_int")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"mo_1e_int": {
|
||||
"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
, "ecp_local" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
, "ecp_non_local" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** Two-electron integrals
|
||||
|
||||
The operators as the same as those defined in the AO two-electron
|
||||
integrals section. Here, the integrals are given in the basis of
|
||||
molecular orbitals.
|
||||
|
||||
#+NAME: mo_2e_int
|
||||
| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
|
||||
| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
|
||||
|
||||
#+CALL: json(data=mo_2e_int, title="mo_2e_int")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"mo_2e_int": {
|
||||
"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* TODO Slater determinants
|
||||
* TODO Reduced density matrices
|
||||
|
||||
#+NAME: rdm
|
||||
| ~one_e~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~one_e_up~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~one_e_dn~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~two_e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ |
|
||||
|
||||
#+CALL: json(data=rdm, title="rdm", last=1)
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"rdm": {
|
||||
"one_e" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||
, "one_e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||
, "one_e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
|
||||
, "two_e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
}
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Appendix :noexport:
|
||||
** Python script from table to json
|
||||
|
||||
#+NAME: json
|
||||
#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
|
||||
print("""#+begin_src python :tangle trex.json""")
|
||||
print(""" "%s": {"""%(title))
|
||||
indent = " "
|
||||
f1 = 0 ; f2 = 0 ; f3 = 0
|
||||
for line in data:
|
||||
line = [ x.replace("~","") for x in line ]
|
||||
name = '"'+line[0]+'"'
|
||||
typ = '"'+line[1]+'"'
|
||||
dims = line[2]
|
||||
if '(' in dims:
|
||||
dims = dims.strip()[1:-1]
|
||||
dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
|
||||
dims = "[ " + ", ".join(dims) + " ]"
|
||||
else:
|
||||
dims = "[ ]"
|
||||
f1 = max(f1, len(name))
|
||||
f2 = max(f2, len(typ))
|
||||
f3 = max(f3, len(dims))
|
||||
|
||||
fmt = "%%s%%%ds : [ %%%ds, %%%ds ]" % (f1, f2, f3)
|
||||
for line in data:
|
||||
line = [ x.replace("~","") for x in line ]
|
||||
name = '"'+line[0]+'"'
|
||||
typ = '"'+line[1]+'"'
|
||||
dims = line[2]
|
||||
if '(' in dims:
|
||||
dims = dims.strip()[1:-1]
|
||||
dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
|
||||
dims = "[ " + ", ".join(dims) + " ]"
|
||||
else:
|
||||
dims = "[]"
|
||||
buffer = fmt % (indent, name, typ.ljust(f2), dims.ljust(f3))
|
||||
indent = " , "
|
||||
print(buffer)
|
||||
|
||||
if last == 0:
|
||||
print(" } ,")
|
||||
else:
|
||||
print(" }")
|
||||
print("""#+end_src""")
|
||||
|
||||
#+end_src
|
||||
|
||||
|
||||
#+begin_src python :tangle trex.json :results output drawer
|
||||
}
|
||||
#+end_src
|
||||
Loading…
Reference in New Issue
Block a user