diff --git a/trex.org b/trex.org index a6f55ee..b9fdc3d 100644 --- a/trex.org +++ b/trex.org @@ -13,6 +13,13 @@ { #+end_src + Dimensions are given both in row-major ~[]~ and column-major ~()~ + formats. Pick the one adapted the the programming language in which + you use TREXIO (Numpy is by default row-major, and Fortran is column-major). + In the column-major representation, ~A(i,j)~ and ~A(i+1,j)~ are + contiguous in memory. In the row-major representation, ~A[i,j]~ and + ~A[i,j+1]~ are contiguous. + * Metadata (metadata group) As we expect TREXIO files to be archived in open-data repositories, @@ -22,15 +29,15 @@ the file, and a textual description. #+NAME: metadata - | Variable | Type | Dimensions (for arrays) | Description | - |-------------------+-------+-------------------------+------------------------------------------| - | ~code_num~ | ~dim~ | | Number of codes used to produce the file | - | ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used | - | ~author_num~ | ~dim~ | | Number of 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 | - | ~description~ | ~str~ | | Text describing the content of file | - | ~unsafe~ | ~int~ | | ~1~: true, ~0~: false | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-------------------+-------+-------------------------+-------------------------+------------------------------------------| + | ~code_num~ | ~dim~ | | | Number of codes used to produce the file | + | ~code~ | ~str~ | ~[metadata.code_num]~ | ~(metadata.code_num)~ | Names of the codes used | + | ~author_num~ | ~dim~ | | | Number of authors of the file | + | ~author~ | ~str~ | ~[metadata.author_num]~ | ~(metadata.author_num)~ | Names of the authors of the file | + | ~package_version~ | ~str~ | | | TREXIO version used to produce the file | + | ~description~ | ~str~ | | | Text describing the content of file | + | ~unsafe~ | ~int~ | | | ~1~: true, ~0~: false | **Note:** The ~unsafe~ attribute of the ~metadata~ group indicates whether the file has been previously opened with ~'u'~ mode. It is @@ -62,14 +69,14 @@ given in Cartesian $(x,y,z)$ format. #+NAME: nucleus - | Variable | Type | Dimensions | Description | - |---------------+---------+-------------------+--------------------------| - | ~num~ | ~dim~ | | Number of nuclei | - | ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei | - | ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms | - | ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels | - | ~point_group~ | ~str~ | | Symmetry point group | - | ~repulsion~ | ~float~ | | Nuclear repulsion energy | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | | + |---------------+---------+----------------------+-------------------------+--------------------------+---| + | ~num~ | ~dim~ | | | Number of nuclei | | + | ~charge~ | ~float~ | ~[nucleus.num]~ | ~(nucleus.num)~ | Charges of the nuclei | | + | ~coord~ | ~float~ | ~[nucleus.num, 3]~ | ~(3, nucleus.num)~ | Coordinates of the atoms | | + | ~label~ | ~str~ | ~[nucleus.num]~ | ~(nucleus.num)~ | Atom labels | | + | ~point_group~ | ~str~ | | | Symmetry point group | | + | ~repulsion~ | ~float~ | | | Nuclear repulsion energy | | #+CALL: json(data=nucleus, title="nucleus") #+RESULTS: @@ -92,15 +99,15 @@ used in periodic calculations. #+NAME: cell - | Variable | Type | Dimensions | Description | - |----------+---------+------------+--------------------------------------------------------------------------| - | ~a~ | ~float~ | ~(3)~ | First real space lattice vector | - | ~b~ | ~float~ | ~(3)~ | Second real space lattice vector | - | ~c~ | ~float~ | ~(3)~ | Third real space lattice vector | - | ~G_a~ | ~float~ | ~(3)~ | First reciprocal space lattice vector | - | ~G_b~ | ~float~ | ~(3)~ | Second reciprocal space lattice vector | - | ~G_c~ | ~float~ | ~(3)~ | Third reciprocal space lattice vector | - | ~two_pi~ | ~int~ | | ~0~ or ~1~. If ~two_pi=1~, $2\pi$ is included in the reciprocal vectors. | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |----------+---------+----------------------+-------------------------+--------------------------------------------------------------------------| + | ~a~ | ~float~ | ~[3]~ | ~(3)~ | First real space lattice vector | + | ~b~ | ~float~ | ~[3]~ | ~(3)~ | Second real space lattice vector | + | ~c~ | ~float~ | ~[3]~ | ~(3)~ | Third real space lattice vector | + | ~G_a~ | ~float~ | ~[3]~ | ~(3)~ | First reciprocal space lattice vector | + | ~G_b~ | ~float~ | ~[3]~ | ~(3)~ | Second reciprocal space lattice vector | + | ~G_c~ | ~float~ | ~[3]~ | ~(3)~ | Third reciprocal space lattice vector | + | ~two_pi~ | ~int~ | | | ~0~ or ~1~. If ~two_pi=1~, $2\pi$ is included in the reciprocal vectors. | #+CALL: json(data=cell, title="cell") @@ -125,10 +132,10 @@ defined in this group. #+NAME: pbc - | Variable | Type | Dimensions | Description | - |------------+---------+------------+-------------------------| - | ~periodic~ | ~int~ | | ~1~: true or ~0~: false | - | ~k_point~ | ~float~ | ~(3)~ | $k$-point sampling | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |------------+---------+----------------------+-------------------------+-------------------------| + | ~periodic~ | ~int~ | | | ~1~: true or ~0~: false | + | ~k_point~ | ~float~ | ~[3]~ | ~(3)~ | $k$-point sampling | #+CALL: json(data=pbc, title="pbc") @@ -158,11 +165,11 @@ #+NAME:electron - | Variable | Type | Dimensions | Description | - |----------+-------+------------+-------------------------------------| - | ~num~ | ~dim~ | | Number of electrons | - | ~up_num~ | ~int~ | | Number of \uparrow-spin electrons | - | ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |----------+-------+----------------------+-------------------------+-------------------------------------| + | ~num~ | ~dim~ | | | Number of electrons | + | ~up_num~ | ~int~ | | | Number of \uparrow-spin electrons | + | ~dn_num~ | ~int~ | | | Number of \downarrow-spin electrons | #+CALL: json(data=electron, title="electron") #+RESULTS: @@ -190,14 +197,14 @@ The ~id~ and ~current_label~ attributes need to be specified for each file. #+NAME: state - | Variable | Type | Dimensions | Description | - |-----------------+---------+---------------+---------------------------------------------------------------------------------------------| - | ~num~ | ~dim~ | | Number of states (including the ground state) | - | ~id~ | ~index~ | | Index of the current state (0 is ground state) | - | ~energy~ | ~float~ | | Energy of the current state | - | ~current_label~ | ~str~ | | Label of the current state | - | ~label~ | ~str~ | ~(state.num)~ | Labels of all states | - | ~file_name~ | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------+---------+----------------------+-------------------------+---------------------------------------------------------------------------------------------| + | ~num~ | ~dim~ | | | Number of states (including the ground state) | + | ~id~ | ~index~ | | | Index of the current state (0 is ground state) | + | ~energy~ | ~float~ | | | Energy of the current state | + | ~current_label~ | ~str~ | | | Label of the current state | + | ~label~ | ~str~ | ~[state.num]~ | ~(state.num)~ | Labels of all states | + | ~file_name~ | ~str~ | ~[state.num]~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) | #+CALL: json(data=state, title="state") @@ -220,7 +227,7 @@ *** Gaussian and Slater-type orbitals - We consider here basis functions centered on nuclei. Hence, it is + We consider here basis functions centered on nuclei. Hence, it is possibile to define /dummy atoms/ to place basis functions in arbitrary positions. @@ -257,10 +264,10 @@ All the basis set parameters are stored in one-dimensional arrays. *** Numerical orbitals - + Trexio supports numerical atom centered orbitals. The implementation is - based on the approach of FHI-aims [Blum, V. et al; Ab initio molecular - simulations with numeric atom-centered orbitals; Computer Physics + based on the approach of FHI-aims [Blum, V. et al; Ab initio molecular + simulations with numeric atom-centered orbitals; Computer Physics Communications 2009]. These orbitals are defined by the atom they are centered on, their angular momentum and a radial function $R_s$, which is of the form @@ -271,7 +278,7 @@ grid. It is constructed to vanish for any $\mathbf{r}$ outside of the grid. The reference points are stored in ~nao_grid_r~ and ~nao_grid_phi~. Additionaly, a separate spline for the first and second - derivative of $u(\mathbf{r})$ can be stored in ~nao_grid_grad~ and ~nao_grid_lap~. + derivative of $u(\mathbf{r})$ can be stored in ~nao_grid_grad~ and ~nao_grid_lap~. Storing them in this form allows to calculate the actual first and second derivatives easily as follows: @@ -307,7 +314,7 @@ \] For convenience, this conversion and functions to evaluate the splines are provided with trexio. Since these implementations are not adapted to - a specific software architecture, a programm using these orbitals should + a specific software architecture, a programm using these orbitals should reimplement them with consideration for its specific needs. *** Plane waves @@ -326,32 +333,32 @@ *** Data definitions #+NAME: basis - | Variable | Type | Dimensions | Description | | - |---------------------+---------+-----------------------------------------------+------------------------------------------------------------------------------+---| - | ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | | - | ~prim_num~ | ~dim~ | | Total number of primitives | | - | ~shell_num~ | ~dim~ | | Total number of shells | | - | ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals | | - | ~interp_coeff_cnt~ | ~dim~ | | Number of coefficients for the numerical orbital interpolator | | - | ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices | | - | ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta | | - | ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) | | - | ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) | | - | ~nao_grid_start~ | ~index~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital | | - | ~nao_grid_size~ | ~dim~ | ~(basis.shell_num)~ | Number of data points per numerical orbital | | - | ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | | - | ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | | - | ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | | - | ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | | - | ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations | | - | ~nao_grid_radius~ | ~float~ | ~(basis.nao_grid_num)~ | Radii of grid points for numerical orbitals | | - | ~nao_grid_phi~ | ~float~ | ~(basis.nao_grid_num)~ | Wave function values for numerical orbitals | | - | ~nao_grid_grad~ | ~float~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals | | - | ~nao_grid_lap~ | ~float~ | ~(basis.nao_grid_num)~ | Laplacian of numerical orbitals | | - | ~interpolator_kind~ | ~str~ | | Kind of spline, e.g. "Polynomial" | | - | ~interpolator_phi~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital interpolation function | | - | ~interpolator_grad~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital gradient interpolation function | | - | ~interpolator_lap~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function | | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |---------------------+---------+------------------------------------------------+------------------------------------------------+------------------------------------------------------------------------------| + | ~type~ | ~str~ | | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | + | ~prim_num~ | ~dim~ | | | Total number of primitives | + | ~shell_num~ | ~dim~ | | | Total number of shells | + | ~nao_grid_num~ | ~dim~ | | | Total number of grid points for numerical orbitals | + | ~interp_coeff_cnt~ | ~dim~ | | | Number of coefficients for the numerical orbital interpolator | + | ~nucleus_index~ | ~index~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices | + | ~shell_ang_mom~ | ~int~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta | + | ~shell_factor~ | ~float~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) | + | ~r_power~ | ~int~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) | + | ~nao_grid_start~ | ~index~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital | + | ~nao_grid_size~ | ~dim~ | ~[basis.shell_num]~ | ~(basis.shell_num)~ | Number of data points per numerical orbital | + | ~shell_index~ | ~index~ | ~[basis.prim_num]~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | + | ~exponent~ | ~float~ | ~[basis.prim_num]~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | + | ~coefficient~ | ~float~ | ~[basis.prim_num]~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | + | ~prim_factor~ | ~float~ | ~[basis.prim_num]~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | + | ~e_cut~ | ~float~ | | | Energy cut-off for plane-wave calculations | + | ~nao_grid_radius~ | ~float~ | ~[basis.nao_grid_num]~ | ~(basis.nao_grid_num)~ | Radii of grid points for numerical orbitals | + | ~nao_grid_phi~ | ~float~ | ~[basis.nao_grid_num]~ | ~(basis.nao_grid_num)~ | Wave function values for numerical orbitals | + | ~nao_grid_grad~ | ~float~ | ~[basis.nao_grid_num]~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals | + | ~nao_grid_lap~ | ~float~ | ~[basis.nao_grid_num]~ | ~(basis.nao_grid_num)~ | Laplacian of numerical orbitals | + | ~interpolator_kind~ | ~str~ | | | Kind of spline, e.g. "Polynomial" | + | ~interpolator_phi~ | ~float~ | ~[basis.nao_grid_num, basis.interp_coeff_cnt]~ | ~(basis.interp_coeff_cnt, basis.nao_grid_num)~ | Coefficients for numerical orbital interpolation function | + | ~interpolator_grad~ | ~float~ | ~[basis.nao_grid_num, basis.interp_coeff_cnt]~ | ~(basis.interp_coeff_cnt, basis.nao_grid_num)~ | Coefficients for numerical orbital gradient interpolation function | + | ~interpolator_lap~ | ~float~ | ~[basis.nao_grid_num, basis.interp_coeff_cnt]~ | ~(basis.interp_coeff_cnt, basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function | @@ -360,32 +367,32 @@ #+RESULTS: :results: #+begin_src python :tangle trex.json - "basis": { - "type" : [ "str" , [] ] - , "prim_num" : [ "dim" , [] ] - , "shell_num" : [ "dim" , [] ] - , "nao_grid_num" : [ "dim" , [] ] - , "interp_coeff_cnt" : [ "dim" , [] ] - , "nucleus_index" : [ "index", [ "basis.shell_num" ] ] - , "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ] - , "shell_factor" : [ "float", [ "basis.shell_num" ] ] - , "r_power" : [ "int" , [ "basis.shell_num" ] ] - , "nao_grid_start" : [ "index", [ "basis.shell_num" ] ] - , "nao_grid_size" : [ "dim" , [ "basis.shell_num" ] ] - , "shell_index" : [ "index", [ "basis.prim_num" ] ] - , "exponent" : [ "float", [ "basis.prim_num" ] ] - , "coefficient" : [ "float", [ "basis.prim_num" ] ] - , "prim_factor" : [ "float", [ "basis.prim_num" ] ] - , "e_cut" : [ "float", [] ] - , "nao_grid_radius" : [ "float", [ "basis.nao_grid_num" ] ] - , "nao_grid_phi" : [ "float", [ "basis.nao_grid_num" ] ] - , "nao_grid_grad" : [ "float", [ "basis.nao_grid_num" ] ] - , "nao_grid_lap" : [ "float", [ "basis.nao_grid_num" ] ] - , "interpolator_kind" : [ "str" , [] ] - , "interpolator_phi" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] - , "interpolator_grad" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] - , "interpolator_lap" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] - } , + "basis": { + "type" : [ "str" , [] ] + , "prim_num" : [ "dim" , [] ] + , "shell_num" : [ "dim" , [] ] + , "nao_grid_num" : [ "dim" , [] ] + , "interp_coeff_cnt" : [ "dim" , [] ] + , "nucleus_index" : [ "index", [ "basis.shell_num" ] ] + , "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ] + , "shell_factor" : [ "float", [ "basis.shell_num" ] ] + , "r_power" : [ "int" , [ "basis.shell_num" ] ] + , "nao_grid_start" : [ "index", [ "basis.shell_num" ] ] + , "nao_grid_size" : [ "dim" , [ "basis.shell_num" ] ] + , "shell_index" : [ "index", [ "basis.prim_num" ] ] + , "exponent" : [ "float", [ "basis.prim_num" ] ] + , "coefficient" : [ "float", [ "basis.prim_num" ] ] + , "prim_factor" : [ "float", [ "basis.prim_num" ] ] + , "e_cut" : [ "float", [] ] + , "nao_grid_radius" : [ "float", [ "basis.nao_grid_num" ] ] + , "nao_grid_phi" : [ "float", [ "basis.nao_grid_num" ] ] + , "nao_grid_grad" : [ "float", [ "basis.nao_grid_num" ] ] + , "nao_grid_lap" : [ "float", [ "basis.nao_grid_num" ] ] + , "interpolator_kind" : [ "str" , [] ] + , "interpolator_phi" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] + , "interpolator_grad" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] + , "interpolator_lap" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ] + } , #+end_src :end: @@ -487,16 +494,16 @@ prim_factor = See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info. #+NAME: ecp - | Variable | Type | Dimensions | Description | - |----------------------+---------+-----------------+----------------------------------------------------------------------------------------| - | ~max_ang_mom_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max}+1$, one higher than the max angular momentum in the removed core orbitals | - | ~z_core~ | ~int~ | ~(nucleus.num)~ | Number of core electrons to remove per atom | - | ~num~ | ~dim~ | | Total number of ECP functions for all atoms and all values of $\ell$ | - | ~ang_mom~ | ~int~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the angular momentum $\ell$ | - | ~nucleus_index~ | ~index~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the atom index | - | ~exponent~ | ~float~ | ~(ecp.num)~ | $\alpha_{A q \ell}$ all ECP exponents | - | ~coefficient~ | ~float~ | ~(ecp.num)~ | $\beta_{A q \ell}$ all ECP coefficients | - | ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |----------------------+---------+----------------------+-------------------------+----------------------------------------------------------------------------------------| + | ~max_ang_mom_plus_1~ | ~int~ | ~[nucleus.num]~ | ~(nucleus.num)~ | $\ell_{\max}+1$, one higher than the max angular momentum in the removed core orbitals | + | ~z_core~ | ~int~ | ~[nucleus.num]~ | ~(nucleus.num)~ | Number of core electrons to remove per atom | + | ~num~ | ~dim~ | | | Total number of ECP functions for all atoms and all values of $\ell$ | + | ~ang_mom~ | ~int~ | ~[ecp.num]~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the angular momentum $\ell$ | + | ~nucleus_index~ | ~index~ | ~[ecp.num]~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the atom index | + | ~exponent~ | ~float~ | ~[ecp.num]~ | ~(ecp.num)~ | $\alpha_{A q \ell}$ all ECP exponents | + | ~coefficient~ | ~float~ | ~[ecp.num]~ | ~(ecp.num)~ | $\beta_{A q \ell}$ all ECP coefficients | + | ~power~ | ~int~ | ~[ecp.num]~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers | There might be some confusion in the meaning of the $\ell_{\max}$. It can be attributed to the maximum angular momentum occupied in @@ -604,21 +611,21 @@ power = [ Feel free to submit a PR if you find missing options/functionalities. #+NAME: grid - | Variable | Type | Dimensions | Description | - |-----------------+---------+------------------+-------------------------------------------------------------------------| - | ~description~ | ~str~ | | Details about the used quadratures can go here | - | ~rad_precision~ | ~float~ | | Radial precision parameter (not used in some schemes like Krack-Köster) | - | ~num~ | ~dim~ | | Number of grid points | - | ~max_ang_num~ | ~int~ | | Maximum number of angular grid points (for pruning) | - | ~min_ang_num~ | ~int~ | | Minimum number of angular grid points (for pruning) | - | ~coord~ | ~float~ | ~(grid.num)~ | Discretized coordinate space | - | ~weight~ | ~float~ | ~(grid.num)~ | Grid weights according to a given partitioning (e.g. Becke) | - | ~ang_num~ | ~dim~ | | Number of angular integration points (if used) | - | ~ang_coord~ | ~float~ | ~(grid.ang_num)~ | Discretized angular space (if used) | - | ~ang_weight~ | ~float~ | ~(grid.ang_num)~ | Angular grid weights (if used) | - | ~rad_num~ | ~dim~ | | Number of radial integration points (if used) | - | ~rad_coord~ | ~float~ | ~(grid.rad_num)~ | Discretized radial space (if used) | - | ~rad_weight~ | ~float~ | ~(grid.rad_num)~ | Radial grid weights (if used) | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------+---------+----------------------+-------------------------+-------------------------------------------------------------------------| + | ~description~ | ~str~ | | | Details about the used quadratures can go here | + | ~rad_precision~ | ~float~ | | | Radial precision parameter (not used in some schemes like Krack-Köster) | + | ~num~ | ~dim~ | | | Number of grid points | + | ~max_ang_num~ | ~int~ | | | Maximum number of angular grid points (for pruning) | + | ~min_ang_num~ | ~int~ | | | Minimum number of angular grid points (for pruning) | + | ~coord~ | ~float~ | ~[grid.num]~ | ~(grid.num)~ | Discretized coordinate space | + | ~weight~ | ~float~ | ~[grid.num]~ | ~(grid.num)~ | Grid weights according to a given partitioning (e.g. Becke) | + | ~ang_num~ | ~dim~ | | | Number of angular integration points (if used) | + | ~ang_coord~ | ~float~ | ~[grid.ang_num]~ | ~(grid.ang_num)~ | Discretized angular space (if used) | + | ~ang_weight~ | ~float~ | ~[grid.ang_num]~ | ~(grid.ang_num)~ | Angular grid weights (if used) | + | ~rad_num~ | ~dim~ | | | Number of radial integration points (if used) | + | ~rad_coord~ | ~float~ | ~[grid.rad_num]~ | ~(grid.rad_num)~ | Discretized radial space (if used) | + | ~rad_weight~ | ~float~ | ~[grid.rad_num]~ | ~(grid.rad_num)~ | Radial grid weights (if used) | #+CALL: json(data=grid, title="grid") @@ -684,12 +691,12 @@ power = [ #+NAME: ao - | Variable | Type | Dimensions | Description | - |-----------------+---------+------------+--------------------------------------| - | ~cartesian~ | ~int~ | | ~1~: true, ~0~: false | - | ~num~ | ~dim~ | | Total number of atomic orbitals | - | ~shell~ | ~index~ | ~(ao.num)~ | Basis set shell for each AO | - | ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factor $\mathcal{N}_i$ | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------+---------+----------------------+-------------------------+--------------------------------------| + | ~cartesian~ | ~int~ | | | ~1~: true, ~0~: false | + | ~num~ | ~dim~ | | | Total number of atomic orbitals | + | ~shell~ | ~index~ | ~[ao.num]~ | ~(ao.num)~ | Basis set shell for each AO | + | ~normalization~ | ~float~ | ~[ao.num]~ | ~(ao.num)~ | Normalization factor $\mathcal{N}_i$ | #+CALL: json(data=ao, title="ao") @@ -722,18 +729,18 @@ power = [ over atomic orbitals. #+NAME: ao_1e_int - | Variable | Type | Dimensions | Description | - |-----------------------+---------+--------------------+--------------------------------------------------------------------------| - | ~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~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ | - | ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ | - | ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) | - | ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) | - | ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) | - | ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) | - | ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------------+---------+----------------------+-------------------------+--------------------------------------------------------------------------| + | ~overlap~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ | + | ~kinetic~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ | + | ~potential_n_e~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ | + | ~ecp~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ | + | ~core_hamiltonian~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ | + | ~overlap_im~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) | + | ~kinetic_im~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) | + | ~potential_n_e_im~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) | + | ~ecp_im~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) | + | ~core_hamiltonian_im~ | ~float~ | ~[ao.num, ao.num]~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) | #+CALL: json(data=ao_1e_int, title="ao_1e_int") @@ -780,14 +787,14 @@ power = [ \] #+NAME: ao_2e_int - | Variable | Type | Dimensions | Description | - |-----------------------+----------------+---------------------------------------------------+-----------------------------------------------| - | ~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 | - | ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI | - | ~eri_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI | - | ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI | - | ~eri_lr_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------------+----------------+---------------------------------------------------+---------------------------------------------------+-----------------------------------------------| + | ~eri~ | ~float sparse~ | ~[ao.num, ao.num, ao.num, ao.num]~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals | + | ~eri_lr~ | ~float sparse~ | ~[ao.num, ao.num, ao.num, ao.num]~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range electron repulsion integrals | + | ~eri_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors for ERI | + | ~eri_cholesky~ | ~float sparse~ | ~[ao_2e_int.eri_cholesky_num, ao.num, ao.num]~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI | + | ~eri_lr_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors for long range ERI | + | ~eri_lr_cholesky~ | ~float sparse~ | ~[ao_2e_int.eri_lr_cholesky_num, ao.num, ao.num]~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI | #+CALL: json(data=ao_2e_int, title="ao_2e_int") @@ -798,7 +805,7 @@ power = [ "eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ] , "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ] , "eri_cholesky_num" : [ "dim" , [] ] - , "eri_cholesky" : [ "float sparse", [ "ao_2e_int.eri_cholesky_num", "ao.num", "ao.num" ] ] + , "eri_cholesky" : [ "float sparse", [ "ao_2e_int.eri_cholesky_num", "ao.num", "ao.num" ] ] , "eri_lr_cholesky_num" : [ "dim" , [] ] , "eri_lr_cholesky" : [ "float sparse", [ "ao_2e_int.eri_lr_cholesky_num", "ao.num", "ao.num" ] ] } , @@ -808,17 +815,17 @@ power = [ ** Molecular orbitals (mo group) #+NAME: mo - | Variable | Type | Dimensions | Description | - |------------------+---------+--------------------+--------------------------------------------------------------------------| - | ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) | - | ~num~ | ~dim~ | | Number of MOs | - | ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients | - | ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part) | - | ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted | - | ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group | - | ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number | - | ~energy~ | ~float~ | ~(mo.num)~ | For canonical MOs, corresponding eigenvalue | - | ~spin~ | ~int~ | ~(mo.num)~ | For UHF wave functions, 0 is $\alpha$ and 1 is $\beta$ | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |------------------+---------+----------------------+-------------------------+--------------------------------------------------------------------------| + | ~type~ | ~str~ | | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) | + | ~num~ | ~dim~ | | | Number of MOs | + | ~coefficient~ | ~float~ | ~[mo.num, ao.num]~ | ~(ao.num, mo.num)~ | MO coefficients | + | ~coefficient_im~ | ~float~ | ~[mo.num, ao.num]~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part) | + | ~class~ | ~str~ | ~[mo.num]~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted | + | ~symmetry~ | ~str~ | ~[mo.num]~ | ~(mo.num)~ | Symmetry in the point group | + | ~occupation~ | ~float~ | ~[mo.num]~ | ~(mo.num)~ | Occupation number | + | ~energy~ | ~float~ | ~[mo.num]~ | ~(mo.num)~ | For canonical MOs, corresponding eigenvalue | + | ~spin~ | ~int~ | ~[mo.num]~ | ~(mo.num)~ | For UHF wave functions, 0 is $\alpha$ and 1 is $\beta$ | #+CALL: json(data=mo, title="mo") @@ -846,18 +853,18 @@ power = [ the basis of molecular orbitals. #+NAME: mo_1e_int - | Variable | Type | Dimensions | Description | - |-----------------------+---------+--------------------+--------------------------------------------------------------------------| - | ~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~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ | - | ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ | - | ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) | - | ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) | - | ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) | - | ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) | - | ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------------+---------+----------------------+-------------------------+--------------------------------------------------------------------------| + | ~overlap~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ | + | ~kinetic~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ | + | ~potential_n_e~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ | + | ~ecp~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ | + | ~core_hamiltonian~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ | + | ~overlap_im~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) | + | ~kinetic_im~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) | + | ~potential_n_e_im~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) | + | ~ecp_im~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) | + | ~core_hamiltonian_im~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) | #+CALL: json(data=mo_1e_int, title="mo_1e_int") @@ -886,14 +893,14 @@ power = [ the basis of molecular orbitals. #+NAME: mo_2e_int - | Variable | Type | Dimensions | Description | - |-----------------------+----------------+---------------------------------------------------+-----------------------------------------------| - | ~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 | - | ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI | - | ~eri_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, mo_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI | - | ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI | - | ~eri_lr_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, mo_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------------+----------------+---------------------------------------------------+---------------------------------------------------+-----------------------------------------------| + | ~eri~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals | + | ~eri_lr~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range electron repulsion integrals | + | ~eri_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors for ERI | + | ~eri_cholesky~ | ~float sparse~ | ~[mo_2e_int.eri_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI | + | ~eri_lr_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors for long range ERI | + | ~eri_lr_cholesky~ | ~float sparse~ | ~[mo_2e_int.eri_lr_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI | #+CALL: json(data=mo_2e_int, title="mo_2e_int") @@ -941,11 +948,11 @@ power = [ An illustration on how to read determinants is presented in the [[./examples.html][examples]]. #+NAME: determinant - | Variable | Type | Dimensions | Description | - |---------------+------------------+---------------------+--------------------------------------------------------| - | ~num~ | ~dim readonly~ | | Number of determinants | - | ~list~ | ~int special~ | ~(determinant.num)~ | List of determinants as integer bit fields | - | ~coefficient~ | ~float buffered~ | ~(determinant.num)~ | Coefficients of the determinants from the CI expansion | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |---------------+------------------+----------------------+-------------------------+--------------------------------------------------------| + | ~num~ | ~dim readonly~ | | | Number of determinants | + | ~list~ | ~int special~ | ~[determinant.num]~ | ~(determinant.num)~ | List of determinants as integer bit fields | + | ~coefficient~ | ~float buffered~ | ~[determinant.num]~ | ~(determinant.num)~ | Coefficients of the determinants from the CI expansion | #+CALL: json(data=determinant, title="determinant") @@ -977,11 +984,11 @@ power = [ the basis of Slater determinants. #+NAME: csf - | Variable | Type | Dimensions | Description | - |-------------------+------------------+-----------------------------+-----------------------------------------| - | ~num~ | ~dim readonly~ | | Number of CSFs | - | ~coefficient~ | ~float buffered~ | ~(csf.num)~ | Coefficients $C_I$ of the CSF expansion | - | ~det_coefficient~ | ~float sparse~ | ~(determinant.num,csf.num)~ | Projection on the determinant basis | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-------------------+------------------+------------------------------+------------------------------+-----------------------------------------| + | ~num~ | ~dim readonly~ | | | Number of CSFs | + | ~coefficient~ | ~float buffered~ | ~[csf.num]~ | ~(csf.num)~ | Coefficients $C_I$ of the CSF expansion | + | ~det_coefficient~ | ~float sparse~ | ~[csf.num, determinant.num]~ | ~(determinant.num, csf.num)~ | Projection on the determinant basis | #+CALL: json(data=csf, title="csf") @@ -1040,16 +1047,16 @@ power = [ - $\dots$ #+NAME: amplitude - | Variable | Type | Dimensions | Description | - |-----------------+----------------+-------------------------------------------------------------+-------------------------------------------------| - | ~single~ | ~float sparse~ | ~(mo.num,mo.num)~ | Single excitation amplitudes | - | ~single_exp~ | ~float sparse~ | ~(mo.num,mo.num)~ | Exponentialized single excitation amplitudes | - | ~double~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Double excitation amplitudes | - | ~double_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Exponentialized double excitation amplitudes | - | ~triple~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Triple excitation amplitudes | - | ~triple_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized triple excitation amplitudes | - | ~quadruple~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Quadruple excitation amplitudes | - | ~quadruple_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized quadruple excitation amplitudes | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |-----------------+----------------+-------------------------------------------------------------+-------------------------------------------------------------+-------------------------------------------------| + | ~single~ | ~float sparse~ | ~[mo.num,mo.num]~ | ~(mo.num,mo.num)~ | Single excitation amplitudes | + | ~single_exp~ | ~float sparse~ | ~[mo.num,mo.num]~ | ~(mo.num,mo.num)~ | Exponentialized single excitation amplitudes | + | ~double~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Double excitation amplitudes | + | ~double_exp~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Exponentialized double excitation amplitudes | + | ~triple~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Triple excitation amplitudes | + | ~triple_exp~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized triple excitation amplitudes | + | ~quadruple~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Quadruple excitation amplitudes | + | ~quadruple_exp~ | ~float sparse~ | ~[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num]~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized quadruple excitation amplitudes | #+CALL: json(data=amplitude, title="amplitude") @@ -1092,7 +1099,7 @@ power = [ \Gamma_{ijkl}^{\downarrow \downarrow} &=& \langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\beta} | \Psi \rangle \\ \Gamma_{ijkl}^{\uparrow \downarrow} &=& - \langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle + \langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle + \langle \Psi | \hat{a}^{\dagger}_{l\alpha}\, \hat{a}^{\dagger}_{k\beta} \hat{a}_{i\beta}\, \hat{a}_{j\alpha} | \Psi \rangle \\ \end{eqnarray*} and the spin-summed one-body density matrix is @@ -1124,25 +1131,25 @@ power = [ $g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$. #+NAME: rdm - | Variable | Type | Dimensions | Description | - |------------------------+----------------+---------------------------------------------------------+-----------------------------------------------------------------------| - | ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix | - | ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix | - | ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix | - | ~1e_transition~ | ~float~ | ~(mo.num, mo.num, state.num, state.num) | One-particle transition density matrices | - | ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) | - | ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix | - | ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix | - | ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix | - | ~2e_transition~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num, state.num, state.num) | Two-particle transition density matrices | - | ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | - | ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) | - | ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | - | ~2e_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\uparrow) | - | ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | - | ~2e_dndn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\downarrow\downarrow) | - | ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | - | ~2e_updn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\downarrow) | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |------------------------+----------------+----------------------------------------------------------+----------------------------------------------------------+-----------------------------------------------------------------------| + | ~1e~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | One body density matrix | + | ~1e_up~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix | + | ~1e_dn~ | ~float~ | ~[mo.num, mo.num]~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix | + | ~1e_transition~ | ~float~ | ~[state.num, state.num, mo.num, mo.num]~ | ~(mo.num, mo.num, state.num, state.num)~ | One-particle transition density matrices | + | ~2e~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) | + | ~2e_upup~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix | + | ~2e_dndn~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix | + | ~2e_updn~ | ~float sparse~ | ~[mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix | + | ~2e_transition~ | ~float sparse~ | ~[state.num, state.num, mo.num, mo.num, mo.num, mo.num]~ | ~(mo.num, mo.num, mo.num, mo.num, state.num, state.num)~ | Two-particle transition density matrices | + | ~2e_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors | + | ~2e_cholesky~ | ~float sparse~ | ~[rdm.2e_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) | + | ~2e_upup_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors | + | ~2e_upup_cholesky~ | ~float sparse~ | ~[rdm.2e_upup_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\uparrow) | + | ~2e_dndn_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors | + | ~2e_dndn_cholesky~ | ~float sparse~ | ~[rdm.2e_dndn_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\downarrow\downarrow) | + | ~2e_updn_cholesky_num~ | ~dim~ | | | Number of Cholesky vectors | + | ~2e_updn_cholesky~ | ~float sparse~ | ~[rdm.2e_updn_cholesky_num, mo.num, mo.num]~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\downarrow) | #+CALL: json(data=rdm, title="rdm") @@ -1217,7 +1224,7 @@ power = [ \sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, [f_{\text{ee}}(r_{ij})]^p - J_{\text{ee},ij}^\infty \right] \] - + $\delta^{\uparrow\downarrow}_{ij}$ is zero when the electrons $i$ and $j$ have the same spin, and one otherwise. @@ -1242,9 +1249,9 @@ power = [ $J_{\text{eN}}$ and $J_{\text{ee}}$ have an asymptotic value of zero: \[ - J_{\text{eN}}^{\infty} = + J_{\text{eN}}^{\infty} = \frac{a_{1,\alpha}\, \kappa_\alpha^{-1}}{1+a_{2,\alpha}\, - \kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p} + \kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p} \] \[ J_{\text{ee},ij}^{\infty} = @@ -1329,19 +1336,19 @@ power = [ *** Table of values #+name: jastrow - | Variable | Type | Dimensions | Description | - |---------------+---------+---------------------+-----------------------------------------------------------------| - | ~type~ | ~str~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ | - | ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters | - | ~ee_num~ | ~dim~ | | Number of Electron-electron parameters | - | ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters | - | ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters | - | ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters | - | ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters | - | ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter | - | ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter | - | ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances | - | ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |---------------+---------+----------------------+-------------------------+-----------------------------------------------------------------| + | ~type~ | ~str~ | | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ | + | ~en_num~ | ~dim~ | | | Number of Electron-nucleus parameters | + | ~ee_num~ | ~dim~ | | | Number of Electron-electron parameters | + | ~een_num~ | ~dim~ | | | Number of Electron-electron-nucleus parameters | + | ~en~ | ~float~ | ~[jastrow.en_num]~ | ~(jastrow.en_num)~ | Electron-nucleus parameters | + | ~ee~ | ~float~ | ~[jastrow.ee_num]~ | ~(jastrow.ee_num)~ | Electron-electron parameters | + | ~een~ | ~float~ | ~[jastrow.een_num]~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters | + | ~en_nucleus~ | ~index~ | ~[jastrow.en_num]~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter | + | ~een_nucleus~ | ~index~ | ~[jastrow.een_num]~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter | + | ~ee_scaling~ | ~float~ | | | $\kappa$ value in CHAMP Jastrow for electron-electron distances | + | ~en_scaling~ | ~float~ | ~[nucleus.num]~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances | #+CALL: json(data=jastrow, title="jastrow") @@ -1349,17 +1356,17 @@ power = [ :results: #+begin_src python :tangle trex.json "jastrow": { - "type" : [ "str" , [] ] - , "en_num" : [ "dim" , [] ] - , "ee_num" : [ "dim" , [] ] - , "een_num" : [ "dim" , [] ] - , "en" : [ "float" , [ "jastrow.en_num" ] ] - , "ee" : [ "float" , [ "jastrow.ee_num" ] ] - , "een" : [ "float" , [ "jastrow.een_num" ] ] - , "en_nucleus" : [ "index" , [ "jastrow.en_num" ] ] - , "een_nucleus" : [ "index" , [ "jastrow.een_num" ] ] - , "ee_scaling" : [ "float" , [] ] - , "en_scaling" : [ "float" , [ "nucleus.num" ] ] + "type" : [ "str" , [] ] + , "en_num" : [ "dim" , [] ] + , "ee_num" : [ "dim" , [] ] + , "een_num" : [ "dim" , [] ] + , "en" : [ "float", [ "jastrow.en_num" ] ] + , "ee" : [ "float", [ "jastrow.ee_num" ] ] + , "een" : [ "float", [ "jastrow.een_num" ] ] + , "en_nucleus" : [ "index", [ "jastrow.en_num" ] ] + , "een_nucleus" : [ "index", [ "jastrow.een_num" ] ] + , "ee_scaling" : [ "float", [] ] + , "en_scaling" : [ "float", [ "nucleus.num" ] ] } , #+end_src :end: @@ -1375,12 +1382,12 @@ power = [ of $\uparrow$-spin and then all the $\downarrow$-spin. #+name: qmc - | Variable | Type | Dimensions | Description | - |----------+---------+------------------------------+---------------------------------------| - | ~num~ | ~dim~ | | Number of 3N-dimensional points | - | ~point~ | ~float~ | ~(3, electron.num, qmc.num)~ | 3N-dimensional points | - | ~psi~ | ~float~ | ~(qmc.num)~ | Wave function evaluated at the points | - | ~e_loc~ | ~float~ | ~(qmc.num)~ | Local energy evaluated at the points | + | Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | + |----------+---------+------------------------------+------------------------------+---------------------------------------| + | ~num~ | ~dim~ | | | Number of 3N-dimensional points | + | ~point~ | ~float~ | ~[qmc.num, electron.num, 3]~ | ~(3, electron.num, qmc.num)~ | 3N-dimensional points | + | ~psi~ | ~float~ | ~[qmc.num]~ | ~(qmc.num)~ | Wave function evaluated at the points | + | ~e_loc~ | ~float~ | ~[qmc.num]~ | ~(qmc.num)~ | Local energy evaluated at the points | #+CALL: json(data=qmc, title="qmc", last=1) @@ -1410,7 +1417,7 @@ for line in data: name = '"'+line[0]+'"' typ = '"'+line[1]+'"' dims = line[2] - if '(' in dims: + if '[' in dims: dims = dims.strip()[1:-1] dims = [ '"'+x.strip()+'"' for x in dims.split(',') ] dims = "[ " + ", ".join(dims) + " ]" @@ -1426,10 +1433,9 @@ for line in data: name = '"'+line[0]+'"' typ = '"'+line[1]+'"' dims = line[2] - if '(' in dims: + if '[' in dims: dims = dims.strip()[1:-1] dims = [ '"'+x.strip()+'"' for x in dims.split(',') ] - dims.reverse() dims = "[ " + ", ".join(dims) + " ]" else: if dims.strip() != "": @@ -1448,6 +1454,20 @@ print("""#+end_src""") #+end_src + #+RESULTS: json + :results: + #+begin_src python :tangle trex.json + "nucleus": { + "num" : [ "dim" , [] ] + , "charge" : [ "float", [ "nucleus.num" ] ] + , "coord" : [ "float", [ "nucleus.num", "3" ] ] + , "label" : [ "str" , [ "nucleus.num" ] ] + , "point_group" : [ "str" , [] ] + , "repulsion" : [ "float", [] ] + } , + #+end_src + :end: + #+begin_src python :tangle trex.json :results output drawer :exports none }