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The dataset must be stored in a phono3py-yaml-like file, e.g., `phono3py_params.yaml`. Use {ref}`--cf3 ` and {ref}`--sp ` option simultaneously. -4. Develop MLPs. At this step `phono3py.pmlp` is saved. +4. Develop MLPs. By default, 90 and 10 percents of the dataset are used for the + training and test, respectively. At this step `phono3py.pmlp` is saved. 5. Generate displacements in supercells either systematic or random displacements. 6. Evaluate MLPs for forces of the supercells generated in step 5. 7. Calculate force constants from displacement-force dataset from steps 5 and 6. @@ -244,7 +245,7 @@ Having `phono3py_params.yaml`, phono3py is executed with `--pypolymlp` option, | |_) | | | | (_) | | | | (_) |__) | |_) | |_| | | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, | |_| |_| |___/ - 3.5.0-dev22+g575c4107 + 3.5.0 -------------------------[time 2024-09-19 15:33:23]------------------------- Compiled with OpenMP support (max 10 threads). @@ -327,3 +328,40 @@ displacements are generated. These displacements are then inverted, resulting in an additional 200 supercells. In total, 400 supercells are created. The forces for these supercells are then evaluated. Finally, the force constants are calculated using symfc. + +## Parameters for developing MLPs + +A few parameters can be specified using the `--mlp-params` option for the +development of MLPs. The parameters are provided as a string, e.g., + +```bash +% phono3py-load phono3py_params.yaml --pypolymlp --mlp-params="ntrain=80, ntest=20" +``` + +Parameters are separated by commas for configuration. A brief explanation of the +available parameters can be found in the docstring of `PypolymlpParams` that is +found by + +```python +In [1]: from phonopy.interface.pypolymlp import PypolymlpParams + +In [2]: help(PypolymlpParams) +``` + +`ntrain` and `ntest` are implemented in phono3py, while the remaining parameters +are directly passed to pypolymlp. Optimizing pypolymlp parameters can be +difficult, both in terms of achieving accuracy and managing the computational +resources required. The current default parameters are likely suitable for +systems up to ternary compounds. For binary systems, the calculations can +generally be run on standard laptop computers, but for ternary systems, around +40 GB of memory or more may be necessary. + +For parameter adjustments, it is recommended to consult the +[pypolymlp](https://github.com/sekocha/pypolymlp) documentation and review the + relevant research papers. + +### `ntrain` and `ntest` + +This method provides a straightforward dataset split: the first `ntrain` +supercells from the list are used for training, while the last `ntest` +supercells are reserved for testing. diff --git a/pypolymlp.html b/pypolymlp.html index b54801e7..777fc8ec 100644 --- a/pypolymlp.html +++ b/pypolymlp.html @@ -331,6 +331,10 @@

Contents

  • Steps 4-6: Force constants calculation (random displacements in step 5)
    • +
  • Parameters for developing MLPs +
    • @@ -374,7 +378,8 @@

    Workflow

  • Prepare dataset composed of displacements, forces, and energies in supercells. The dataset must be stored in a phono3py-yaml-like file, e.g., phono3py_params.yaml. Use –cf3 and –sp option simultaneously.

    • -

  • Develop MLPs. At this step phono3py.pmlp is saved.

    • +

  • Develop MLPs. By default, 90 and 10 percents of the dataset are used for the +training and test, respectively. At this step phono3py.pmlp is saved.

  • Generate displacements in supercells either systematic or random displacements.

  • Evaluate MLPs for forces of the supercells generated in step 5.

  • Calculate force constants from displacement-force dataset from steps 5 and 6.

    • @@ -567,7 +572,7 @@

    Steps 4-6: Force constants calculation (random displacements in step 5)| |_) | | | | (_) | | | | (_) |__) | |_) | |_| | | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, | |_| |_| |___/ - 3.5.0-dev22+g575c4107 + 3.5.0 -------------------------[time 2024-09-19 15:33:23]------------------------- Compiled with OpenMP support (max 10 threads). @@ -651,6 +656,38 @@

    Steps 4-6: Force constants calculation (random displacements in step 5) +
    +

    Parameters for developing MLPs#

    +

    A few parameters can be specified using the --mlp-params option for the +development of MLPs. The parameters are provided as a string, e.g.,

    +
    % phono3py-load phono3py_params.yaml --pypolymlp --mlp-params="ntrain=80, ntest=20"
+
    +
    +

    Parameters are separated by commas for configuration. A brief explanation of the +available parameters can be found in the docstring of PypolymlpParams that is +found by

    +
    In [1]: from phonopy.interface.pypolymlp import PypolymlpParams
+
+In [2]: help(PypolymlpParams)
+
    +
    +

    ntrain and ntest are implemented in phono3py, while the remaining parameters +are directly passed to pypolymlp. Optimizing pypolymlp parameters can be +difficult, both in terms of achieving accuracy and managing the computational +resources required. The current default parameters are likely suitable for +systems up to ternary compounds. For binary systems, the calculations can +generally be run on standard laptop computers, but for ternary systems, around +40 GB of memory or more may be necessary.

    +

    For parameter adjustments, it is recommended to consult the +pypolymlp documentation and review the +relevant research papers.

    +
    +

    ntrain and ntest#

    +

    This method provides a straightforward dataset split: the first ntrain +supercells from the list are used for training, while the last ntest +supercells are reserved for testing.

    +
    +
    @@ -705,6 +742,10 @@

    Steps 4-6: Force constants calculation (random displacements in step 5)Steps 4-6: Force constants calculation (random displacements in step 5) +
  • Parameters for developing MLPs +
    • diff --git a/searchindex.js b/searchindex.js index 0102592b..ccfa471e 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"--alm": [[4, "alm"]], "--amplitude (DISPLACEMENT_DISTANCE)": [[4, "amplitude-displacement-distance"]], "--ave-pp (USE_AVE_PP = .TRUE.)": [[4, "ave-pp-use-ave-pp-true"]], "--average": [[1, "average"]], "--bi (BAND_INDICES)": [[4, "bi-band-indices"]], "--boundary-mfp, --bmfp (BOUNDARY_MFP)": [[4, "boundary-mfp-bmfp-boundary-mfp"]], "--br (BTERTA = .TRUE.)": [[4, "br-bterta-true"]], "--cf2 (command option only)": [[4, "cf2-command-option-only"]], "--cf3 (command option only)": [[4, "cf3-command-option-only"]], "--cf3-file (command option only)": [[4, "cf3-file-command-option-only"]], "--cfc or --compact-fc (COMPACT_FC = .TRUE.)": [[4, "cfc-or-compact-fc-compact-fc-true"]], "--cfs or --create-force-sets (command option only)": [[4, "cfs-or-create-force-sets-command-option-only"]], "--cfz (command option only)": [[4, "cfz-command-option-only"]], "--cmap": [[1, "cmap"]], "--const-ave-pp (CONST_AVE_PP = .TRUE.)": [[4, "const-ave-pp-const-ave-pp-true"]], "--crystal (CALCULATOR = CRYSTAL)": [[4, "crystal-calculator-crystal"]], "--cutoff, --fmax": [[1, "cutoff-fmax"]], "--cutoff-fc3 or --cutoff-fc3-distance (CUTOFF_FC3_DISTANCE)": [[4, "cutoff-fc3-or-cutoff-fc3-distance-cutoff-fc3-distance"]], "--cutoff-pair or --cutoff-pair-distance (CUTOFF_PAIR_DISTANCE)": [[4, "cutoff-pair-or-cutoff-pair-distance-cutoff-pair-distance"]], "--cv": [[1, "cv"]], "--dim (DIM)": [[4, "dim-dim"]], "--dim-fc2 (DIM_FC2)": [[4, "dim-fc2-dim-fc2"]], "--dos": [[1, "dos"]], "--dr, --density-ratio": [[1, "dr-density-ratio"]], "--fc-calc, --fc-calculator (FC_CALCULATOR)": [[4, "fc-calc-fc-calculator-fc-calculator"]], "--fc-calc-opt, --fc-calculator-options (FC_CALCULATOR_OPTIONS)": [[4, "fc-calc-opt-fc-calculator-options-fc-calculator-options"]], "--fc-symmetry (FC_SYMMETRY = .TRUE.)": [[4, "fc-symmetry-fc-symmetry-true"]], "--fc2 (READ_FC2 = .TRUE.)": [[4, "fc2-read-fc2-true"]], "--fc3 (READ_FC3 = .TRUE.)": [[4, "fc3-read-fc3-true"]], "--fs2f2 or --force-sets-to-forces-fc2 (command option only)": [[4, "fs2f2-or-force-sets-to-forces-fc2-command-option-only"]], "--full-pp (FULL_PP = .TRUE.)": [[4, "full-pp-full-pp-true"]], "--ga (GRID_ADDRESSES)": [[4, "ga-grid-addresses"]], "--gamma": [[1, "gamma"]], "--gp (GRID_POINTS)": [[4, "gp-grid-points"]], "--gruneisen (GRUNEISEN = .TRUE.)": [[4, "gruneisen-gruneisen-true"]], "--gv": [[1, "gv"]], "--gv-norm": [[1, "gv-norm"]], "--hdf5-compression (command option only)": [[4, "hdf5-compression-command-option-only"]], "--io (command option only)": [[4, "io-command-option-only"]], "--ise (IMAG_SELF_ENERGY = .TRUE.)": [[4, "ise-imag-self-energy-true"]], "--isotope (ISOTOPE =.TRUE.)": [[4, "isotope-isotope-true"]], "--jdos (JOINT_DOS = .TRUE.)": [[4, "jdos-joint-dos-true"]], "--lbte (LBTE = .TRUE.)": [[4, "lbte-lbte-true"]], "--magmom (MAGMOM)": [[4, "magmom-magmom"]], "--mass (MASS)": [[4, "mass-mass"]], "--mass-variances or --mv (MASS_VARIANCES)": [[4, "mass-variances-or-mv-mass-variances"]], "--mesh (MESH or MESH_NUMBERS)": [[4, "mesh-mesh-or-mesh-numbers"]], "--mfp": [[1, "mfp"]], "--nac (NAC = .TRUE.)": [[4, "nac-nac-true"]], "--nbins": [[1, "nbins"]], "--nsp": [[1, "nsp"]], "--nu (N_U = .TRUE.)": [[4, "nu-n-u-true"]], "--num-freq-points, --freq-pitch (NUM_FREQUENCY_POINTS)": [[4, "num-freq-points-freq-pitch-num-frequency-points"]], "--pa, --primitive-axes (PRIMITIVE_AXES)": [[4, "pa-primitive-axes-primitive-axes"]], "--pqj": [[1, "pqj"]], "--q-direction (Q_DIRECTION)": [[4, "q-direction-q-direction"]], "--qe (CALCULATOR = QE)": [[4, "qe-calculator-qe"]], "--rd (RANDOM_DISPLACEMENTS), --rd-fc2 (RANDOM_DISPLACEMENTS_FC2) and --random-seed (RANDOM_SEED)": [[4, "rd-random-displacements-rd-fc2-random-displacements-fc2-and-random-seed-random-seed"]], "--read-gamma (READ_GAMMA = .TRUE.)": [[4, "read-gamma-read-gamma-true"]], "--read-phonon (READ_PHONON = .TRUE.)": [[4, "read-phonon-read-phonon-true"]], "--rse (REAL_SELF_ENERGY = .TRUE.)": [[4, "rse-real-self-energy-true"]], "--scattering-event-class (SCATTERING_EVENT_CLASS)": [[4, "scattering-event-class-scattering-event-class"]], "--sigma (SIGMA)": [[4, "sigma-sigma"]], "--sigma-cutoff (SIGMA_CUTOFF_WIDTH)": [[4, "sigma-cutoff-sigma-cutoff-width"]], "--sp or --save-params": [[4, "sp-or-save-params"]], "--spf (SPECTRAL_FUNCTION = .TRUE.)": [[4, "spf-spectral-function-true"]], "--stp (command option only)": [[4, "stp-command-option-only"]], "--symfc and --alm": [[4, "symfc-and-alm"]], "--tau": [[1, "tau"]], "--temperature": [[1, "temperature"], [1, "id2"]], "--thm (TETRAHEDRON = .TRUE.)": [[4, "thm-tetrahedron-true"]], "--tmax, --tmin, --tstep (TMAX, TMIN, TSTEP)": [[4, "tmax-tmin-tstep-tmax-tmin-tstep"]], "--trace": [[1, "trace"]], "--ts (TEMPERATURES): Temperatures": [[4, "ts-temperatures-temperatures"]], "--turbomole (CALCULATOR = TURBOMOLE)": [[4, "turbomole-calculator-turbomole"]], 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[[21, "a-practical-way-to-check-lattice-thermal-conductivity-result"]], "A script extract supercell IDs from phono3py_disp.yaml": [[6, "a-script-extract-supercell-ids-from-phono3py-disp-yaml"]], "Acknowledgements": [[11, "acknowledgements"]], "AlN-LDA": [[6, "aln-lda"]], "Apr-16-2016: version 1.10.7": [[2, "apr-16-2016-version-1-10-7"]], "Apr-18-2019: Version 1.17.0": [[2, "apr-18-2019-version-1-17-0"]], "Apr-19-2024: Version 3.0.0": [[2, "apr-19-2024-version-3-0-0"]], "Apr-20-2024: Version 3.0.1": [[2, "apr-20-2024-version-3-0-1"]], "Apr-21-2024: Version 3.0.2": [[2, "apr-21-2024-version-3-0-2"]], "Apr-24-2016: version 1.10.9": [[2, "apr-24-2016-version-1-10-9"]], "Apr-3-2023: Version 2.6.0": [[2, "apr-3-2023-version-2-6-0"]], "Apr-9-2022: Version 2.3.0": [[2, "apr-9-2022-version-2-3-0"]], "Aug-12-2015: version 0.9.12": [[2, "aug-12-2015-version-0-9-12"]], "Aug-23-2024: Version 3.4": [[2, "aug-23-2024-version-3-4"]], "Aug-6-2024: Version 3.3.3": [[2, "aug-6-2024-version-3-3-3"]], 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"fc-calc-opt-fc-calculator-options-fc-calculator-options"]], "--fc-symmetry (FC_SYMMETRY = .TRUE.)": [[4, "fc-symmetry-fc-symmetry-true"]], "--fc2 (READ_FC2 = .TRUE.)": [[4, "fc2-read-fc2-true"]], "--fc3 (READ_FC3 = .TRUE.)": [[4, "fc3-read-fc3-true"]], "--fs2f2 or --force-sets-to-forces-fc2 (command option only)": [[4, "fs2f2-or-force-sets-to-forces-fc2-command-option-only"]], "--full-pp (FULL_PP = .TRUE.)": [[4, "full-pp-full-pp-true"]], "--ga (GRID_ADDRESSES)": [[4, "ga-grid-addresses"]], "--gamma": [[1, "gamma"]], "--gp (GRID_POINTS)": [[4, "gp-grid-points"]], "--gruneisen (GRUNEISEN = .TRUE.)": [[4, "gruneisen-gruneisen-true"]], "--gv": [[1, "gv"]], "--gv-norm": [[1, "gv-norm"]], "--hdf5-compression (command option only)": [[4, "hdf5-compression-command-option-only"]], "--io (command option only)": [[4, "io-command-option-only"]], "--ise (IMAG_SELF_ENERGY = .TRUE.)": [[4, "ise-imag-self-energy-true"]], "--isotope (ISOTOPE =.TRUE.)": [[4, "isotope-isotope-true"]], "--jdos (JOINT_DOS = .TRUE.)": [[4, "jdos-joint-dos-true"]], "--lbte (LBTE = .TRUE.)": [[4, "lbte-lbte-true"]], "--magmom (MAGMOM)": [[4, "magmom-magmom"]], "--mass (MASS)": [[4, "mass-mass"]], "--mass-variances or --mv (MASS_VARIANCES)": [[4, "mass-variances-or-mv-mass-variances"]], "--mesh (MESH or MESH_NUMBERS)": [[4, "mesh-mesh-or-mesh-numbers"]], "--mfp": [[1, "mfp"]], "--nac (NAC = .TRUE.)": [[4, "nac-nac-true"]], "--nbins": [[1, "nbins"]], "--nsp": [[1, "nsp"]], "--nu (N_U = .TRUE.)": [[4, "nu-n-u-true"]], "--num-freq-points, --freq-pitch (NUM_FREQUENCY_POINTS)": [[4, "num-freq-points-freq-pitch-num-frequency-points"]], "--pa, --primitive-axes (PRIMITIVE_AXES)": [[4, "pa-primitive-axes-primitive-axes"]], "--pqj": [[1, "pqj"]], "--q-direction (Q_DIRECTION)": [[4, "q-direction-q-direction"]], "--qe (CALCULATOR = QE)": [[4, "qe-calculator-qe"]], "--rd (RANDOM_DISPLACEMENTS), --rd-fc2 (RANDOM_DISPLACEMENTS_FC2) and --random-seed (RANDOM_SEED)": [[4, 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"o-command-option-only"]], "3x3 integer matrix (experimental)": [[15, "x3-integer-matrix-experimental"]], "A convenient script": [[26, "a-convenient-script"]], "A practical way to check lattice thermal conductivity result": [[21, "a-practical-way-to-check-lattice-thermal-conductivity-result"]], "A script extract supercell IDs from phono3py_disp.yaml": [[6, "a-script-extract-supercell-ids-from-phono3py-disp-yaml"]], "Acknowledgements": [[11, "acknowledgements"]], "AlN-LDA": [[6, "aln-lda"]], "Apr-16-2016: version 1.10.7": [[2, "apr-16-2016-version-1-10-7"]], "Apr-18-2019: Version 1.17.0": [[2, "apr-18-2019-version-1-17-0"]], "Apr-19-2024: Version 3.0.0": [[2, "apr-19-2024-version-3-0-0"]], "Apr-20-2024: Version 3.0.1": [[2, "apr-20-2024-version-3-0-1"]], "Apr-21-2024: Version 3.0.2": [[2, "apr-21-2024-version-3-0-2"]], "Apr-24-2016: version 1.10.9": [[2, "apr-24-2016-version-1-10-9"]], "Apr-3-2023: Version 2.6.0": [[2, "apr-3-2023-version-2-6-0"]], "Apr-9-2022: Version 2.3.0": [[2, "apr-9-2022-version-2-3-0"]], "Aug-12-2015: version 0.9.12": [[2, "aug-12-2015-version-0-9-12"]], "Aug-23-2024: Version 3.4": [[2, "aug-23-2024-version-3-4"]], "Aug-6-2024: Version 3.3.3": [[2, "aug-6-2024-version-3-3-3"]], "Aug-8-2024: Version 3.3.4": [[2, "aug-8-2024-version-3-3-4"]], "Auxiliary tools": [[1, null]], "Averaged phonon-phonon interaction strength": [[20, "averaged-phonon-phonon-interaction-strength"]], "Brillouin zone integration": [[4, "brillouin-zone-integration"]], "Brillouin zone summation": [[21, "brillouin-zone-summation"]], "Build with automatic search of library configurations by cmake": [[13, "build-with-automatic-search-of-library-configurations-by-cmake"]], "CRYSTAL & phono3py calculation": [[5, null]], "Calculation of force constants": [[19, "calculation-of-force-constants"]], "Calculator interface": [[4, "calculator-interface"]], "Calculator specific behaviors": [[14, "calculator-specific-behaviors"]], "Change Log": [[2, null]], "Changes in version 0.6.0": 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