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Merge pull request #86 from TREX-CoE/pseudo

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Pseudo
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Anthony Scemama 2022-03-02 22:54:46 +01:00 committed by GitHub
commit dfad23d362
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4 changed files with 20 additions and 24 deletions
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2
CMakeLists.txt
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@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
# Initialize the CMake project.
project(Trexio
VERSION 2.1.0
VERSION 2.2.0
DESCRIPTION "TREX I/O library"
LANGUAGES C Fortran
)

1
ChangeLog
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@ -4,6 +4,7 @@ CHANGES
2.2
---
- Merged local and non-local pseudopotential integrals in #86
- Fixed backwards incompatibility of the `TREXIO_TEXT` back end in #82
- Added `TREXIO_AUTO` back end for read-only mode (`r`) in PR #80
- Added unsafe mode (`u`) to `trexio_open`. When enabled, data can be

2
configure.ac
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@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.69])
AC_INIT([trexio],[2.1.0],[https://github.com/TREX-CoE/trexio/issues])
AC_INIT([trexio],[2.2.0],[https://github.com/TREX-CoE/trexio/issues])
AC_CONFIG_SRCDIR([Makefile.in])
AC_CONFIG_HEADERS([include/config.h])

39
trex.org
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@ -481,22 +481,20 @@ prim_factor =
\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
- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} + \hat{V}_\text{ECP}$ : 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
| 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_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)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
| 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)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
@ -507,8 +505,7 @@ prim_factor =
"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" ] ]
, "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
} ,
#+end_src
@ -587,14 +584,13 @@ prim_factor =
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_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)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
| 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)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
#+CALL: json(data=mo_1e_int, title="mo_1e_int")
@ -605,8 +601,7 @@ prim_factor =
"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" ] ]
, "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
} ,
#+end_src