more text + debug

.gitignore

@@ -2,3 +2,4 @@ docs/src/examples/
 
 *build*
 *egg-info/
+sg_execution_times.rst

docs/src/conf.py

@@ -1,6 +1,7 @@
 # Add any Sphinx extension module names here, as strings.
 extensions = [
     "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
     "sphinx_gallery.load_style",
 ]
 
@@ -12,3 +13,14 @@
 
 htmlhelp_basename = "COSMO software-cookbook"
 html_theme = "furo"
+
+
+intersphinx_mapping = {
+    "ase": ("https://wiki.fysik.dtu.dk/ase/", None),
+    "metatensor": ("https://lab-cosmo.github.io/metatensor/latest/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+    "rascaline": ("https://luthaf.fr/rascaline/latest/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+}

docs/src/index.rst

@@ -9,8 +9,4 @@ COSMO Software Cookbook
    :caption: Table of Contents
    :maxdepth: 1
 
-   examples/roy_gch/roy_gch
-   examples/lode_linear/lode_tutorial
-   examples/sample_selection/sample_selection
-   examples/gaas_map/gaas_map
    examples/cp2k_run_batch/setup_reftraj

examples/cp2k_run_batch/.gitignore

@@ -0,0 +1,2 @@
+production/
+cp2k.out

examples/cp2k_run_batch/README.rst

@@ -2,6 +2,6 @@ CP2K bash computation
 ============================
 
 This is an example of a batch calculation using CP2K.
-The inputs are a set of structures in `./data/example.xyz`
+The inputs are a set of structures in `example.xyz`
 using the parameters defined in `./data/reftraj_template.cp2k`
 importing basisset and pseudopotentials from the local CP2K install.

examples/cp2k_run_batch/cp2k.inp

@@ -0,0 +1,158 @@
+!!! Generated by ASE !!!
+@SET PREP 0
+@SET SCF_GUESS RESTART
+@SET SCREEN_ON_INITIAL_P TRUE
+@IF ${PREP}
+@SET SCF_GUESS ATOMIC
+@SET SCREEN_ON_INITIAL_P FALSE
+@ENDIF
+&MOTION
+   &PRINT
+      &CELL
+         &EACH
+            MD 1
+         &END EACH
+      &END CELL
+      &FORCES
+         &EACH
+            MD 1
+         &END EACH
+      &END FORCES
+   &END PRINT
+   &MD
+      ENSEMBLE REFTRAJ
+      &REFTRAJ
+         EVAL_ENERGY_FORCES TRUE
+         EVAL_FORCES TRUE
+         CELL_FILE_NAME reftraj.cell
+         TRAJ_FILE_NAME reftraj.xyz
+         FIRST_SNAPSHOT 1
+         VARIABLE_VOLUME TRUE
+         LAST_SNAPSHOT 1
+      &END REFTRAJ
+   &END MD
+&END MOTION
+&FORCE_EVAL
+   &PRINT
+      &FORCES
+         &EACH
+            MD 1
+         &END EACH
+      &END FORCES
+   &END PRINT
+   &DFT
+      BASIS_SET_FILE_NAME /opt/homebrew/share/cp2k/data/GTH_BASIS_SETS
+      BASIS_SET_FILE_NAME /opt/homebrew/share/cp2k/data/BASIS_ADMM
+      POTENTIAL_FILE_NAME /opt/homebrew/share/cp2k/data/POTENTIAL
+      &MGRID
+         CUTOFF 400
+      &END MGRID
+      &SCF
+         SCF_GUESS ${SCF_GUESS}
+         MAX_SCF 20
+         EPS_SCF 5.0E-7
+         &OT
+            MINIMIZER DIIS
+            PRECONDITIONER FULL_ALL
+         &END OT
+         &OUTER_SCF
+            MAX_SCF 20
+            EPS_SCF 5.0E-7
+         &END OUTER_SCF
+      &END SCF
+      &QS
+         EPS_DEFAULT 1.0E-12
+         EPS_PGF_ORB 1.0E-16
+         EXTRAPOLATION_ORDER 5
+      &END QS
+      &XC # revPBE0-TC-D3
+         &XC_FUNCTIONAL
+            &PBE
+               PARAMETRIZATION REVPBE
+               SCALE_X 0.75
+               SCALE_C 1.0
+            &END PBE
+         &END XC_FUNCTIONAL
+         &HF
+            FRACTION 0.25
+            &SCREENING
+               EPS_SCHWARZ 1.0E-6
+               SCREEN_ON_INITIAL_P ${SCREEN_ON_INITIAL_P}
+            &END SCREENING
+            &MEMORY
+               MAX_MEMORY 37000
+               EPS_STORAGE_SCALING 0.1
+            &END MEMORY
+            &INTERACTION_POTENTIAL
+               POTENTIAL_TYPE TRUNCATED
+               CUTOFF_RADIUS 3.0
+               T_C_G_DATA /opt/homebrew/share/cp2k/data/t_c_g.dat
+            &END INTERACTION_POTENTIAL
+            &HF_INFO
+            &END HF_INFO
+         &END HF
+         &VDW_POTENTIAL
+            POTENTIAL_TYPE PAIR_POTENTIAL
+            &PAIR_POTENTIAL
+               TYPE DFTD3
+               R_CUTOFF 15
+               LONG_RANGE_CORRECTION TRUE
+               REFERENCE_FUNCTIONAL revPBE0
+               PARAMETER_FILE_NAME /opt/homebrew/share/cp2k/data/dftd3.dat
+            &END PAIR_POTENTIAL
+         &END VDW_POTENTIAL
+         &XC_GRID
+            XC_DERIV SPLINE2
+         &END XC_GRID
+      &END XC
+      &AUXILIARY_DENSITY_MATRIX_METHOD
+         METHOD BASIS_PROJECTION
+         ADMM_PURIFICATION_METHOD MO_DIAG
+      &END AUXILIARY_DENSITY_MATRIX_METHOD
+   &END DFT
+   &SUBSYS
+      &TOPOLOGY
+         COORD_FILE_NAME init.xyz
+         COORD_FILE_FORMAT XYZ
+         CONN_FILE_FORMAT GENERATE
+      &END TOPOLOGY
+      &CELL
+         ABC [angstrom] 3.911173 3.911173 3.911173
+         PERIODIC XYZ
+         A 3.911173230168922377e+00 0.000000000000000000e+00 0.000000000000000000e+00
+         B 0.000000000000000000e+00 3.911173230168922377e+00 0.000000000000000000e+00
+         C 0.000000000000000000e+00 0.000000000000000000e+00 3.911173230168922377e+00
+      &END CELL
+      &KIND H
+         BASIS_SET TZV2P-GTH
+         BASIS_SET AUX_FIT cpFIT3
+         POTENTIAL GTH-PBE-q1
+      &END KIND
+      &KIND O
+         BASIS_SET TZV2P-GTH
+         BASIS_SET AUX_FIT cpFIT3
+         POTENTIAL GTH-PBE-q6
+      &END KIND
+      &KIND Na
+         BASIS_SET TZV2P-GTH
+         BASIS_SET AUX_FIT cpFIT3
+         POTENTIAL GTH-PBE-q9
+      &END KIND
+      &KIND Cl
+         BASIS_SET TZV2P-GTH
+         BASIS_SET AUX_FIT cpFIT3
+         POTENTIAL GTH-PBE-q7
+      &END KIND
+      &COORD
+         H 2.557992919999999781e+00 3.047632299999999961e-01 6.788335399999999575e-01
+         H 1.467392919999999989e+00 5.358410000000000117e-01 3.590156770000000108e+00
+         O 1.786192919999999962e+00 3.826856460000000126e+00 3.117135400000000112e-01
+         H 3.520580310000000157e+00 2.559366770000000013e+00 2.710913230000000063e+00
+         H 8.486338500000000229e-01 2.050096770000000124e+00 1.854526459999999988e+00
+         O 9.813384999999999470e-02 1.756606770000000095e+00 2.338376460000000101e+00
+      &END COORD
+   &END SUBSYS
+&END FORCE_EVAL
+&GLOBAL
+   PROJECT cp2k
+&END GLOBAL

examples/cp2k_run_batch/cp2k_shell.ssmp

@@ -0,0 +1 @@
+/opt/homebrew/bin/cp2k.ssmp

examples/cp2k_run_batch/environement.yml

@@ -1,8 +1,8 @@
 name: cp2k_run_batch
 dependencies:
-  - python=3.11
+  - python=3.10
   - pip
-  - conda-forge/label/cf202003::cp2k 
+  - conda-forge::libopenblas
+  - conda-forge::cp2k
   - pip:
     - ase
-