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PicoCentauriPicoCentauri
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‎.gitignore

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*build*
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*egg-info/
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sg_execution_times.rst

‎docs/src/conf.py

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

‎docs/src/index.rst

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:caption: Table of Contents
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:maxdepth: 1
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examples/roy_gch/roy_gch
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examples/lode_linear/lode_tutorial
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examples/sample_selection/sample_selection
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examples/gaas_map/gaas_map
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examples/cp2k_run_batch/setup_reftraj

‎examples/cp2k_run_batch/.gitignore

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production/
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cp2k.out

‎examples/cp2k_run_batch/README.rst

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

‎examples/cp2k_run_batch/cp2k.inp

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

‎examples/cp2k_run_batch/cp2k_shell.ssmp

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/opt/homebrew/bin/cp2k.ssmp

‎examples/cp2k_run_batch/environement.yml

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name: cp2k_run_batch
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dependencies:
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- python=3.11
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- python=3.10
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- pip
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- conda-forge/label/cf202003::cp2k
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- conda-forge::libopenblas
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- conda-forge::cp2k
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- pip:
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- ase
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‎examples/cp2k_run_batch/data/example.xyz ‎examples/cp2k_run_batch/example.xyz

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‎examples/cp2k_run_batch/data/reftraj_template.cp2k ‎examples/cp2k_run_batch/reftraj_template.cp2k

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