Adds cp2k script

.github/workflows/docs.yml

@@ -25,6 +25,7 @@ jobs:
           python-version: "3.10"
       - name: install dependencies
         run: |
+          sudo apt-get install -y cp2k
           python -m pip install tox
       - name: build documentation
         run: tox -e docs

.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

@@ -13,3 +13,4 @@ COSMO Software Cookbook
    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 +1,5 @@
+production/
+
+cp2k.out
+cp2k.inp
+cp2k_shell.ssmp

examples/cp2k_run_batch/README.rst

@@ -0,0 +1,7 @@
+CP2K bash computation
+============================
+
+This is an example of a batch calculation using CP2K.
+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/environement.yml

@@ -0,0 +1,6 @@
+name: cp2k_run_batch
+dependencies:
+  - python=3.11
+  - pip
+  - pip:
+    - ase

examples/cp2k_run_batch/example.xyz

@@ -0,0 +1,8 @@
+6
+Lattice="3.9111732301689224 0.0 0.0 0.0 3.9111732301689224 0.0 0.0 0.0 3.9111732301689224" Properties=species:S:1:pos:R:3 #=T CELL(abcABC):=T 3.91117=T 90.00000=T Step:=T 1975600=T Bead:=T 0=T x_centroidangstrom=T cellangstrom=T count=0 pbc="T T T"
+H        2.55799292       0.30476323       0.67883354
+H        1.46739292       0.53584100       3.59015677
+O        1.78619292       3.82685646       0.31171354
+H        3.52058031       2.55936677       2.71091323
+H        0.84863385       2.05009677       1.85452646
+O        0.09813385       1.75660677       2.33837646

examples/cp2k_run_batch/reftraj_template.cp2k

@@ -0,0 +1,144 @@
+@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
+
+&GLOBAL
+  PROJECT //PROJECT//
+  PREFERRED_FFT_LIBRARY FFTW
+  FFTW_PLAN_TYPE MEASURE
+  RUN_TYPE MD
+  PRINT_LEVEL LOW
+&END GLOBAL
+
+&MOTION
+  &PRINT
+    &CELL
+      &EACH
+        MD 1
+      &END EACH
+    &END CELL
+    &FORCES
+      &EACH
+        MD 1
+      &END EACH
+    &END FORCES
+  &END PRINT
+  &MD
+    ENSEMBLE REFTRAJ
+    &REFTRAJ  ! Loads an external trajectory file and performs analysis on the loaded snapshots.
+      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 //LAST_SNAPSHOT//
+    &END REFTRAJ
+  &END MD
+&END MOTION
+
+&FORCE_EVAL
+  &PRINT
+    &FORCES
+      &EACH
+        MD 1
+      &END EACH
+    &END FORCES
+  &END PRINT
+  &DFT
+    BASIS_SET_FILE_NAME GTH_BASIS_SETS
+    BASIS_SET_FILE_NAME BASIS_ADMM
+    POTENTIAL_FILE_NAME 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
+      &END XC_FUNCTIONAL
+      &HF
+        FRACTION 0.25
+        &SCREENING
+          EPS_SCHWARZ 1.0E-6
+          SCREEN_ON_INITIAL_P ${SCREEN_ON_INITIAL_P}
+        &END
+        &MEMORY
+          MAX_MEMORY 37000
+          EPS_STORAGE_SCALING 0.1
+        &END
+        &INTERACTION_POTENTIAL
+          POTENTIAL_TYPE TRUNCATED
+          CUTOFF_RADIUS 3.0
+          T_C_G_DATA t_c_g.dat
+        &END
+        &HF_INFO
+        &END HF_INFO
+      &END
+      &VDW_POTENTIAL
+         POTENTIAL_TYPE PAIR_POTENTIAL
+         &PAIR_POTENTIAL
+            TYPE DFTD3
+            R_CUTOFF 15
+            LONG_RANGE_CORRECTION TRUE
+            REFERENCE_FUNCTIONAL revPBE0
+            PARAMETER_FILE_NAME dftd3.dat
+         &END
+      &END
+      &XC_GRID
+        XC_DERIV SPLINE2
+      &END
+    &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] //CELL//
+    &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
+  &END SUBSYS
+&END FORCE_EVAL

examples/cp2k_run_batch/run_calcs.sh

@@ -0,0 +1,8 @@
+#! /bin/bash
+
+for i in $(find ./production/ -mindepth 1 -type d); do
+    cd $i
+    cp2k -i in.cp2k
+    cd -
+done
+